To begin with, this I believe is a Vampyrellid — a group of voracious predatory amoebae belonging to the Rhizaria supergroup, which is one of the three major groups of amoebae. Other groups include the Amoebozoa (as the name may suggest) and Heteroloboseans in Excavata (of which the so-called “brain-eating” (misnomer alert) Naegleria fowlerii is a proud member). Amoebae or at least some amoeboid characteristics are found in almost all the other groups as well, and it appears that protists as a whole could care less about our yearnings to classify them as ‘amoeba’ or ‘flagellate’. So in the centre of this vampyrellid we see a vesicular nucleus — vaguely doughnut-shaped, but with a thick core where the hole should go (more like a danish, perhaps?). There is also a have digested diatom sitting around. Above the amoeba is a Stramenopile flagellate, perhaps Spumella sp. or something. Those too can be quite malleable and amoeboidy, despite being ‘flagellates’ to us.

Staying in Rhizaria, here is a short timelapse of a cercomonad (Cercomonas sp?), a common denizen of soil ecosystems, but here found in a pond sample. Note how stretchy and squishy it is, and how its thin pseudopodia (filopodia) tend to branch a bit. Cercomonads are really fun to watch, and have been reported to gang up on the much larger nematodes and kill them, seemingly for later grazing upon the bacteria that grow on their corpses (Bjørnlund & Rønn 2008). Microbes don’t seem to care much for our ‘food chain’ concept either. (There’s also a recent report of marine dinoflagellates ganging up on small crustaceans and devouring them!)

The next amoeba I will stick somewhere between Rhizaria and Amoebozoa, which is roughly equivalent to be uncertain about whether something is a plant or an animal, as far as evolutionary distances go. Basically, this is a crazy skinny amoeba with lots of thin pseudopodia, some branching and fusing. And I’m serious about the skinny part — it appears to be around a couple microns thick at most, and I’ve seen specimens over 100 microns wide. It’s extremely dynamic, both in wiggling its pseudopodia but also in circulating the cytoplasm. The contents slosh about rather wildly.

Here’s a glimpse of a different, much larger specimen — which I am fairly confident should be the same thing, but may well be wrong. Note how the pseudopodia branch and fuse, giving it a rather off shape. The pseudopodia on the right are freshly retracted, giving them a thicker, bubblier appearance as there is a fair bit of extra membrane material there. The behaviour is a bit Rhizarian-like, but there is this somewhat annoying group of Amoebozoans, the Varioseans, that can basically do whatever they want — including mimicking Rhizarians to make our lives harder. This amoeba might be Biomyxa sp. (Rhizarian), or Leptomyxa sp. (Variosean) — probably can’t say without sequence, or at least a healthy dose of experience.

Now you may wonder… where is it’s, you know, stuff, given how thin it is. Surely, it must have some sort of nuclei and vacuoles and various other things a eukaryote must have. I think one can barely make out its nuclei, with a healthy dose of imagination: indicated here by arrowheads:

This amoeba appears to have another morphology, perhaps more common in nature — as there aren’t too many cover slips floating around in the wild to provide flat surfaces (water surface may work though — the water side of the air-water interface is covered in numerous ‘benthic’ species, including amoebae, because life — and physics — is very different on the scale of microns). Here this amoeba (or something different altogether, for all I know) is seen gathering up clumps of diatoms and generally being thicker as it floats around in the water, as opposed to being stuck to glass. I hope it eats those diatoms.

By the way, this particular group of amoebae comes from a 5 month old sample from a Chicago pond (Jackson Park Lagoon) that was sitting around on my bench, amongst a metropolis of other seemingly-abandoned petri dish condominiums. Yes, I can pretend my bench mess has a purpose now — take that, labmates!

Now for something more normal — an amoebozoan amoeba that has gathered up a clump of empty diatom shells around like a test. This may be an arcellinid (group of amoebae known for building elaborate shells), but the way it moves would make it a rather awkward one. In any case, I think it’s pretty!

A random small amoebozoan amoeba. Can’t really say what this is without sequence data. I think you can barely make out a nucleus-like structure towards the right, between the clear cytoplasm (ectoplasm) and the more granular/filled stuff (endoplasm). If that is the nucleus, it’s definitely in the endoplasm, for the record. There are tons of tiny amoebae crawling around in practically everything, and many of them are completely ignored because of their tendency to look like slide gunk. One of the most common marine amoebae, Parvamoeba, hasn’t been described until the early 90′s, even though it has probably been unknowingly seen by hundreds before that. It’s so small and inconspicuous that most have probably dismissed it as slide gunk. I wonder if some of them might harbour substantially less-inconspicuous genomic and cellular madness, if only somebody looked…

And lastly, a gratuitous spirotrich ciliate, that has nothing to do with amoebae. Next to it is a small flagellate of the cryptomonad affinity — Chilomonas sp. Its group is photosynthetic, but this one lost photosynthetic abilities and is left with colourless plastids. The ciliate has a couple macronuclei paired with micronuclei, the latter being actually visible as clear roundish things in the top left image. Note that this poor ciliate is a bit squished, and it would normally be less blobby in shape.

It took a while, but after finally attaining the necessary potentially-overpriced fancy pieces of glass, the lab scope can now take acceptable DIC images. Meaning yours truly can once again slightly misappropriate lab resources during strange hours of the night and stare at protists ‘from the wild’. I return with a bucket of images to gradually unload upon y’all, a couple at a time. Hopefully this’ll gradually massage this dessicated writing brain into eventually oozing out more informative posts. Oh, and if anyone asks — science is hard. Just thought I’d share that.

First off, because we love squishy things, an amoeba. Not sure which one this is (those bastards are notoriously full of attitude when it comes to identifying them by shape… possibly because their shapes are so dynamic, and our brains just suck at processing that), but in the left frame you can see little nubby protrusions sticking out of the flattened pseudopodium. These disappeared after some time. I’m not sure what exactly prompted this amoeba to have goosebumps (podbumps?) on its pseudopod, but some well-prepared SEMs (electron micrographs, in 3D) show that even the classical Amoeba proteus isn’t as smooth and gooey as it looks — the critter is lined with tiny microvilli, much like your intestine. I must add here that there is still much to learn about motility in free-living amoebae — while much of the classical cell biology has been done in Amoebozoan amoebae, the modern molecular cell biology largely focuses on animal cell cultures, which are quite derived, and very much not self-sufficient. The image on the right shows another optical section through the same amoeba. The prominent round thing in the middle, with a bulge inside, is its nucleus — you can almost make out the unusually thick envelope, and the bulge in the middle should be a wad of densely packed chromatin constituting the nucleolus. I wonder what the speck in the middle of that is… One could also make out some food vesicles, as well as a half-digested diatom. I suspect the very clear bottom-most vesicle is the contractile vacuole, which acts much like our kidneys do in regulating osmotic pressure within the cell (so it doesn’t explode).

(click the images to enlarge)

Our next critter is a member of one of my favourite groups of ciliates: the spirotrichs. Spirotrichs are awesome: not only do they have cilia bundled up into adorable little “feet” (cirri) — with which they quite literally walk along surfaces — their nuclei (yes, plural) are weird. Even by ciliate standards. The ‘boring’ ciliate way of doing nuclei involves carrying two types of them: a small one that gets carried around and transmitted through generations, but not transcribed; and a large one that is transcribed, but destroyed and created anew each time it mates. There’s a whole clusterfuck of epigenetics between the small germline nucleus and the new large somatic nucleus that is created from it, and in spirotrichs it has led to chunks of the genome being scrambled in the germline nucleus. Before the somatic nucleus can use it properly, the segments of the genome have to be cut up and placed in the right order so the genes are legible. There’s more on gene scrambling in this post on Aspidisca, another spirotrich (of a subgroup that doesn’t do that, but I needed an excuse to ramble about it there at the time). Also, did I mention spirotrichs are just plain CUTE? (the bottom centre frame has two granular somatic nuclei visible in the middle; to the right of the top somatic nucleus in the bottom right image lies a relatively large germline nucleus; in most other ciliate groups this nucleus is much harder to see)

Speaking of Aspidisca, here are a couple of them hanging out with some random flagellates (prominent one with long plates on it is a euglenid):

As far as protists go, ciliates like to have lots of sex, or else their somatic nucleus decays without replacement (some ciliates can, ummm, deal with mate shortages on their own — but those are rare, though quite convenient in the lab). However, as one might expect, sometimes sex can go horribly, horribly wrong. This pair of spirotrichs has gone too far and fused their entire front ends (where the mouth ciliature is, right of image) — unfortunately, this adventure has proven to be a lethal one. The nuclei here are fragmented for meiosis and are difficult to resolve, although I do think I see some fragments between the end of the ‘mouth’ (thing with lines across it — those are special oral cilia) and the contractile vacuole just below the fusion of the two tails. I should probably consider labeling these next time…

And lastly, something a bit more familiar, by being a fellow animal: a rotifer. At its front end to the right are the cilia which it uses to form water currents (and fool some students, schoolteachers…and zoologists (in the 19th century anyway) into thinking it’s a ciliate); just below those are the jaws that are hard to see — look for the structure with a line running down the middle, where the two of them meet. Then there’s a bunch of big multicellular organs I know nothing about, and towards the posterior end, just above the toes, is what someone pointed out to be an ovary. Unfortunately, that’s the extent of my rotifer knowledge, although I do know this one is not one of the permanently asexual Bdelloid rotifers.

That’s it for this round, but there will be plenty more to come! And maybe even a real post in a little while.

Of course, we later learn about very large bacteria, and very small protists, and the non-insignificant overlap between the two (this also happens between animals and protists — Polilov 2011 Arthropod Struc Dev). Ranging from 200-800 microns, Epulopiscium, a bacterial denizen of fish guts, is so massive, it was initially mistaken for a protist (Montgomery & Pollack 1988 J Eukaryotic Microbiol)! To give you a sense of scale, here’s a fairly famous image showing the giant next to Paramecium (also quite big for a protist, even) and E.coli reduced to tiny specks in the background.Conversely, eukaryotes can get quite tiny. Micromonas, as its name may suggest, is a tiny green alga that thrives in the oceans. It is so incredibly small that one can only marvel at how the minimal set of vital organelles is crammed in there like in miniature Japanese electronics. A similarly sized critter, Ostreococcus, doesn’t have room for extra microtubules to fit in, and does mitosis with fewer ‘tubes than chromosomes (recall that in the classic mitotic spindle, each chromosome gets its special bundle of microtubules).  Point is, at less than 2 microns, this eukaryote is smaller than many prokaryotes. And there’s a large and every-growing group of these ‘picoeukaryotes’ distributed across many phyla, most still unseen and only known from environmental DNA sequences.

The max-min size ranges for the various protist supergroups, and bacteria, have been compiled into a handy figure from a paper quite relevantly titled Protists are microbes too: a perspective, arguing that mainstream microbiologists(=bacteriologists) need not shun their pets’ eukaryotic neighbours based on size alone — eukaryotes can be no less ‘micro’ than prokaryotes!

All that said, size does matter, and eukaryotes are largely bigger than prokaryotes. If the above figure were replaced by a box plot, this point would become clearer. This issue shows up a fair bit in discussions of eukaryogenesis, or the origin and early evolution of eukaryotes. For one very basic thing, chomping on bacteria by engulfing them (phagocytosis — a key ability of eukaryotes) sort of requires the chomper to be bigger than the chompee — although some protists have a remarkable ability to engulf and devour critters bigger than themselves, presumably by recruiting lots of extra membrane. Being big can also help keep you away from becoming chomped upon yourself. Again, generally: it doesn’t help the nematode much as it suffocates in the digestive vacuole of a Vampyrellid amoeba. We can assume that in some circumstances, getting bigger may well be favoured by selection. But then we wonder: why don’t bacteria typically get bigger? Instead of getting murdered by the thousands, why can’t the Klebsiella in my Paramecium cultures simply get bigger and gleefully watch the ciliates choke on it?

The common explanation is that they simply can’t. Physical constrains have [mostly] forever locked the prokaryotic cell within a certain size. It needed to first acquire something special, something a eukaryote has, before its bloated form could even be viable. The special eukaryotic thing can be argued to be, among many others, the mitochondrion, supplying enough energy to maintain the bloated cell, or the cytoskeleton, providing structural support for the cell. Presumably, they both have a role, and perhaps the rarity of large bacteria can be in large part explained by biophysical limitations, both structural and energetic. But some, like our friend in the fish gut, can still get big. What I’ve been wondering about lately is do bacteria really need to be big?

Perhaps what may constrain bacterial size isn’t just biophysical properties, but also ‘evolutionary’ properties — namely the presumed trade-off between size and replication rate. Generally, you can’t both grow and reproduce simultaneously, and any time you spend making your cell larger is time you spend not dividing. I’m not one for frivolous adaptationist explanations, but this trade-off would have a pretty damn direct effect on fitness: the growth rate would be directly reduced in a population where cells spend more of their time getting big. In other words, if it’s real, it will probably matter. Furthermore, a reduction in reproductive rate may shrink your effective population size (crudely skipping a few important factors like carrying capacity), which weakens the relative strength of selection vs. drift, leading to deleterious mutation accumulation, etc. In other words, getting big does not come cheap. And in addition to physical constrains, one must also consider population genetic ones: all other things equal, a competition between individuals from a larger population versus those from a smaller one would probably more often grant victory to those of the larger one. The quantitatively-challenged group would suffer from a bad case of genetic load.

But why, then, don’t bacteria that are now ruthlessly hunted in the post-eukaryogenesis world finally have enough selective pressure to grow bigger? Biophysical constraints do play a crucial role in general, but we should also weigh those factors with the evolutionary side of things. Perhaps in the grand scheme of things, the selective pressure by predation just isn’t big enough to sacrifice precious replication time for growth. Or maybe it is — who knows? We can speculate (loudly!) about this for years and years, but speculation can inspire potentially interesting experiments. And yes, you can do experiments in evolution, thankfully. For example, one could try to evolve bacteria, under more or less equal effective population sizes, with and without various predators (small enough that they’d choke on a slightly bigger bacterium). Will size be selected upon? Of course if it isn’t, you can’t rule out physical constraints. You could try to artificially select for larger bacteria, but that might be a logistic nightmare, given how tiny they are. You could fiddle with their cell cycle machinery to grow larger cells, and compete them against smaller counterparts in the presence or absense of predators. You could then fiddle with effective population sizes… there’s plenty of work.

I don’t quite have the patience or expertise for these sorts of experiments (and some must have been done already!). The point here was to remind ourselves that the most obvious explanation can sometimes blind us of less obvious, but potentially important, additional factors. It’s tempting to accept “biophysical constraints” as the catch-all answer to the issue of why bacteria tend to be small, but perhaps something like population size may be involved as well, among other aspects of biology that I’m ignorant of. And this stuff can be spared from the tumultuous world of pure speculation and tested with real experiments. There’s plenty of work to be done!

In the previous post of this series (way too long ago…), we went on a little diving adventure into the microscopic world with our ocelloid-bearing Nematodinium, starting off with giant kelp forests and gradually zooming into the critters living on the blade surfaces and wading deep into the molecular world of genomes — barely scratching the surface, of course. In this installment, we’ll look a little more at how these critters interact with each other — and with bacteria — sometimes with lasting consequences. Perhaps among the more familiar of these relationships is that of eukaryotes with their domesticated cyanobacterium — the plastid (commonly referred to as a chloroplast in plants). Among other metabolic roles, the plastid most importantly converts carbon dioxide (in case of plants, in the form of an atmospheric gas) to a carbon source the organisms can actually use — sugars. The plastids need not be our familiar shades of green, and often lining a rocky sea shore is a colourful spectrum of seaweeds. Perhaps most prominent are the red algae, which use some different pigments and don’t look any shade of green.

Looking up at towering kelp forest above us, we see photosynthetic organisms of yet another colour, ones that have a rather elaborate story to tell. It is not particularly obvious that the reason kelps can harness cyanobacterial phytosynthetic might lies in ancient relatives of the lowly red crust surrounding their holdfasts (‘roots’). Millions of years ago, a predatory eukaryote chomped on a single-celled red alga and kept it (I’m mostly lying — but bear with me, for the sake of brevity!) — this red alga lost its nucleus and became a secondary plastid endosymbiont. What followed is an explosion of algal diversity, encompassing organisms as disparate as scale-forming haptophytes, dinoflagellates, glass-encased diatoms, apicomplexan parasites like the malaria pathogen, and our giant multicellular kelps. Even seemingly definitively un-algal things like ciliates and fungal-like oomycetes appear to have been photosynthetic in their distant past. Collectively, the plastids of these organisms are referred to as ‘brown’, owing to their often brownish appearance — the kelps as an obvious showcase.

One group of these brown algae, although perhaps brown from a separate red algal plastid symbiosis event, has a remnant nucleus of the ex-red algal slave. These flagellates, called cryptomonads, have an extremely shrunken second nucleus (a ‘nucleomorph’, even) associated with the plastid — these nucleomorph genomes are famous among the molecular evolution folks for their extremely compact, streamlined genomes, with very few, short introns and small intergenic regions. In other words, whatever factors were responsible for causing a shrinkage of the nucleomorph genome led to a massive purging of junk DNA sequences that most eukaryotic genomes are festering with.

Dinophysis, a dinoflagellate, caught in the act of sucking stolen cryptomonad plastids out of a ciliate, Myrionecta. (Park et al. 2006 Aquat Microb Ecol)

Like most good things, plastids can also be stolen. And repackaged. And sometimes stolen again. We watch a herd of cryptomonads casually swirling about, soaking up the final rays of daylight. Suddenly, into the midst of the frolicking algae jumps a sizeable ciliate, and devours a cryptomonad. It then proceeds to separate out the plastid with its nucleomorph and other associates, as well as the cryptomonad nucleus — and packages them together into a vesicle! Presumably, in this manner, the ciliate prolongs the use of its stolen photosynthetic equipment by keeping its original life support nearby.

Those who partake in the life of crime must seldom let their guard down, however — for they have plenty of colleagues hell-bent on acquiring a taste of their freshly stolen wealth. We may gasp as Dinophysis, a dinoflagellate, suddenly descends upon the ciliate thief and stabs it with a straw. You can see individual stolen plastids, ex-cryptomonads, being sucked up through this straw and into the dinoflagellate. Not only is this dino itself a thief, it can’t do its criminals activities independently — apparently, the cryptomonads are toxic to Dinophysis unless tamed by the ciliate. Alterntively, cryptomonads are quite fast, and perhaps the sluggish Dinophysis simply cannot catch up to them — the ciliate, Myrionecta, has been known to jump.

It may be particularly perplexing that Dinophysis generally seems to come with its own plastids. For a long time, people have attempted to culture Dinophysis like its fellow photosynthetic dino brethren, assuming it should be perfectly capable of living off sunlight and a nutritious medium. For many years this elusive (and often beautiful!) organism could not be cultured. The discovery of its strange association with Myrionecta and cryptomonads enabled them to finally be cultured, but it remains an open question whether they do have their own plastids and merely supplement them with theft, or subsist entire on stolen goods. This story is discussed in somewhat greater detail in this post on the other blog, and remains an active research topic.

Photosynthesis is not the only wealth sought after in symbiotic relationships, and our story will continue next time as we meet more bacterial denizens of protistan cells, following a brief encounter with a tertiary plastid endosymbiont, just to drive the point home that symbiosis, while not necessarily by any means a ‘fundamental driving force’ in evolution, is a fairly common and important phenomenon. It’s just too easy, one you maintain a constant partner within yourself, to become dependent upon it.

But now I’m back in a very evolution-ey place, just in time for a collection of equally evolution-ey posts from all four corners of the internet! (tubes have corners, right? No? Oh…)

Apologies if I missed any; there are a lot of submissions this month… will correct noted omissions and errors!

Population Biology and Incertae Sedis

“Nothing in evolution makes sense except in light of population genetics” (Mike Lynch (2007) in PNAS )

A post from Larry Moran’s Sandwalk using English history, of all things, to explain the difference between population size (N) and effective population size (Ne), a key distinction in population biology. If you’ve happened to be following the discussion of non-adaptive evolution on my other blog at all, this may be particularly relevant, especially in light of populations being actually finite and not everything being due to selection. [/shameless scientific agenda-pushing]

* It totally looked like there was a crapload of stuff on population biology when I looked at the list of submissions, but apparently looks can deceive, and I now look like an idiot… but, again,  looks can deceive!

Sarah Hird at Nothing In Biology Makes Sense talks about a remarkable study where gut microbiota in flies have been shown to influence their mating behaviour!

Ken Weiss at The Mermaid’s Tale on the Darwinian Method, it’s contributions to biology as well as its drawbacks.

Suzanne Elvidge at Genome Engineering announces the completion of a clover genome and its publication in Nature.

Bradly Alicea at Synthetic Daisies discusses the principle of overproduction in biology as a way to enhance dispersal and dissipation. Bradly then reviews neutral networks and their interplay with robustness and selection.

Speciation and biogeography

*Don’t let this heading lead you into thinking I don’t believe in sympatric speciation!

Jerry Coyne at Why Evolution is True rightly rails against the hideous phrase “species with no relatives”, a big pet peeve of mine as well. Everything here is related, unless you can support a separate abiogenesis event! Jerry also talks about inbreeding and pleiotropy in the [artificial] evolution of the Cocker Spaniel, pointing out how quickly evolution can happen and showing once again that it’s not all just a theory.

Bjørn Østman at Pleiotropy explains the difference between Biological and Ecological Species Concepts (two of several, I must add), and why we should be explicit in which one we use. Bjørn also manages to tie in speciation with the happenings in the virtual social world: for example, the competition between Google+ and Facebook has seemingly led to a niche differentiation between the two. Amazing how fundamental evolutionary principles apply far beyond just biological evolution, apparently indifferent to the lack of nucleic acids.

The species concept conundrum does not end yet! Benjamin Haller at Evo-Eco Eco-Evo discusses speciation — and magic! — in Darwin’s finches.

Noah Mattoon at Nothing in Biology Makes Sense discusses the perplexing issue of greater taxonomic diversity at lower latitudes — the explanation for which, of course, must have roots in evolution.

Tom Houslay at Nothing In Biology Makes Sense talks about leks (mating displays) and exaggerated traits, and the ‘lek paradox’ of runaway selection rendering the displays practically useless in terms of picking out genetically fitter mates.

Kevin Zelnio at EcoEvoLab on the manifest destiny of rats, or more precisely — the multiple independent origins of the black rats’ cohabitation with humans.

Continuing on with the theme of creatures everyone adores and admires, Craig McClain at Deep Sea News enviously fantasises about hagfish sex life talks about the notorious hagfish defense mechanism: spewing out bucketloads (literally) of slime to clog the attacker’s gills. Or, as Craig calls it, “slimepocalypse”.

Lynn Margulis

While Margulis’ connections with symbiogenesis and crackpot theories has perhaps been beaten to death by now, she was also perhaps the closest thing protistologists had to a public figure, despite disagreeing with her on almost everything. Promoting and attracting serious attention to Mereschkowsky’s theory of the symbiotic origins of plastids (Bill Martin’s translation to English, PDF) was no small contribution in itself, but she also published books like Handbook of the Protoctista*, a valuable (if taxonomically flawed in places) resource on various protistan phyla. Full of ‘undilopodia’, of course. As much as we scoff at her terminology and rather outlandish theories, what other modern comprehensive source is out there on protistology, besides the Illustrated Guide to Protozoology (almost exclusively taxonomic) and Klaus Haussman and coauthors’ Protistology textbook?

* If only a second edition could still come out… and the first edition is not only out of print, but the unsold copies were *destroyed* by the publisher a while back!

But you’re not here to read my ramblings… (I should write a post at some point, on her connections with protistology and eukaryogenesis theories)

Suzanne Elvige at Genome Engineering is among those breaking the news that Lynn Margulis passed away at age 73 due to a stroke. And of course, such an outlier of a scientist attracts some exceptionally crappy journalism (although not outlier so much…). Greg Mayer at Why Evolution is True corrects the notion that Margulis’ symbiogensis theory somehow contradicts Darwinism and completely revolutionises evolutionary theory as we know it.

Braaaains…and homonids

Ed Yong at Not Exactly Rocket Science discusses the gut size vs. brain size trade-off in humans.

EE Georgi at Chimeras talks about transposon activity in brain cells and its resemblance to McClintock’s corn kernel variation.

Iddo Friedberg at Byte Size Biology talks about de novo (completely new) genes in humans, of which there is apparently an extant handful, if the bioinformatics data are to be trusted. These genes may contribute to explaining some of the differences between humans and our closest relatives.

Anne Buchanan at The Mermaid’s Tale entertains the idea that our African homonid ancestors ate insects, in contrast with the more glorious-sounding notion of “Man the Hunter”.

Scott Lee at Scott Free Thinking argues for paleolithic diets and avoidance of post-agricultural starchy foods.

Eric Johnson at The Primate Diaries talks about the impacts of social networks on relative brain size, and a surprising finding of a correlation between human brain structure the the extent of online social networking.

Greg Laden talks about the difference between Behavioural Biology and Evolutionary Psychology, and lists a few enticing books we should read.

Hannah Waters at Culturing Science has a captivating post about the biology of grief and mourning, touching on mass mourning of Steve Jobs as well as a personal example.

Crushing the Corpse of Creationism*

*We wish… sigh.

Jack Scanlan at Homologous Legs on rhetoricotrophism (awesome term!) of Intelligent Design creationism, and why we should be less dismissive and ridicule-obsessed when addressing their claims. (furthermore, I think ID/creationist movements unintentionally do a good job at pointing out the failings in our teaching of evolution…)

Michael Barton at The Dispersal of Darwin corrects three outrageous oft-cited creationist quotemines of The Origin. Michael also showcases a beautifully-illustrated book on our origins, Bang! How we came to be, for children. Lastly, there’s also a nice video featuring various scientists and educators talking about the importance of evolution.

BEACON Researchers at Work series

There’s a neat series of posts written by postdocs and graduate students about their research at the BEACON consortium:

Jenna Gallie talks about her research on the effects of varying rates of environmental change on adaptation in E.coli.

Justin Meyer talks about co-evolution of the lambda phage with its victim host E.coli.

Furthermore, Martina Ederer makes synthetic viruses to reconstruct ancestral viral genomes.

That’s it (I think) for this month’s Carnival of Evolution. The next edition will be at THE EBB & FLOW on 01 January. Please use this submission form to contribute entries about things pertaining to evolutionary biology.

And I am working on my post debts! Working full time in research appears to be having a deleterious effect on my blogging these days…

*Yeah, yeah, Archaea included, we can argue about that later…

As a protistologist and some sort of a cell biologist by modest training, I am particularly interested in cellular evolution. In other words, while some focus on the evolution of macroscopic structures like wings and organs, and others look at molecular evolution of proteins and DNA sequences, I am especially fascinated by the in-between, or how subcellular structures themselves evolve. Unlike molecular biologists, we don’t have the luxury of compressing the bulk of our data into sequences, and unlike developmental biologists, we can’t really fiddle with gene expression patterns and play with a variety of well-established mutants, both natural (visible diversity) and lab-generated. This is partly why there’s a chance you probably never heard of evolutionary cell biology as a field. The other big problem is that much of cellular diversity is, in fact, microbial, and microbial eukaryotes are barely studied (yeasts excluded — but they’re secondarily unicellular anyway, and really, really weird). It is in the unicellular protist realm where the cell is at its finest, for it cannot cower behind the multitudes of defective cell types of a multicellular organism to get by, and must be largely self-sufficient. (This is illustrated further by the higher average complexity (diversity of cell parts) in a unicellular cell than that of multicellular organisms (McShea 2002 Evolution)) Not only are these unicellular organisms cellularly complicated, they’re also quite diverse. Bacteria most definitely have a cell biology of their own, but that has become recognised only recently, with the advent of fluorescent, and now super-resolution, light microscopy — where one can finally track labelled proteins in a living cell. Thus, for the moment, evolutionary cell biology is ultimately the cell biology of protists in light of evolution.

Of course, just comparing cell structures and marvelling at their diversity isn’t really all there is to exploring the evolution of something. Even reconstructing ancestral states is just the beginning. Evolutionary biology ultimately pursues mechanisms — the more general, the better. We could simply assume evolution is adaptation  and make up stories as we go along (not entirely unpopular in some circles), but that wouldn’t be good science. Evolution involves introduction of variation through mutation (with its own associated biases) as well as sorting thereof nor only through selection, but also by drift and migration.

Furthermore, heritability is a key required component in evolutionary change, and here we may even get something interesting: transmission of information from one cell to the next (generationally) is not only genomic (or genetic), but also depends on a spatial component. If you simply express a genome in a lipid vesicle, the proteins will not magically self-assemble into a working cell. A chunk of necessary information is directed by the patterning in the cell preceding the division. Extra-nuclear (or extra-genomic) cellular inheritance is not a mere figment of speculative imagination — it has been demonstrated in ciliates in a landmark experiment by Tracy Sonneborn and Janine Beisson: a row of cilia was inverted surgically (presumably without affecting the genome, of course) in a Paramecium, and this strain with a backwards row of cilia persists to this very day, despite multiple genetic outcrossings (Beisson & Sonneborn 1965 PNAS)! Several of Sonneborn’s deciples have continued the work on cytoplasmic inheritance in ciliates, with some fascinating results. However, molecular work on poorly-established model organisms is difficult and frustrating, and until recently bordered on insanity.  Unfortunately, just as the tools for doing molecular and cell biology on more obscure organisms are greatly improving (10 years ago, you couldn’t just sequence a genome on a whim…), the field has largely…retired.

If there is a channel of inheritance that occurs in parallel with classical genetics, this opens up a whole new jungle of tantalising questions and models waiting to be described and later discarded in favour of better ones. While classical quantitative genetics (which studies the inheritance of visible, measurable traits from generation to generation) is a fairly established and well-studied field at this point, a parallel epigenetic system of heritability would call for expansion of the field to include non-genomic quantitative genetics, where it gets rather tricky due to lack of direct digital coding sequences. Of course, if such a thing were to be pursued and studied, it would have to be in unicellular organisms, for they don’t have that pesky bottleneck where the entire multi-million celled creature has to fit through a fertilised egg or seed for later re-patterning. Essentially, this would call for an evolutionary developmental biology of the single cell. While all cells go through something resembling classical development in principle in at least some stage of their lives, we don’t typically think of development on a cellular level. We really should.

Enough with the long-winded theoretical introduction. What, if anything, can we say about the grandest scale of eukaryotic cellular evolution, or that nagging question of how eukaryotes evolved? Unfortunately, as mentioned above, the picture is a little unsettling. That last common ancestor of ours was simply too complex! (creationist quotemining in 3…2…1)

It appears that the last eukaryotic common ancestor (LECA), of all currently known living eukaryotes, has been a fairly sophisticated cell with a nucleus and a mitochondrion, as well as elaborate cytoskeletal and membrane trafficking systems. Presumably, the first eukaryotic common ancestor was drastically less complicated, but its nature remains elusive, and all but one of its descendants...lost. (Also see Field & Dacks 2009 Curr Op Cell Biol)(abbreviations are for major eukaryotic supergroups, in no particular order: Ex - Excavates; Op - Opisthokonts; Am - Amoebozoans; SAR - Stramenopile-Alveolate-Rhizaria clade; Arch - Archaeplastids; Ha - "Hacrobia")

Not only does LECA appear to possess a mitochondrion and a modern nucleus, but it already has a sophisticated membrane trafficking system, a cytoskeleton, capacity to devour prey by phagocytosis, a eukaryotic cell cycle regulation system, meiotic sex, and even a flagellum. Not only does it have modern-looking structures, but it seems to have already used many of the same molecular components used in a variety of living eukaryotes today. As an aside, you may perhaps recall having learned cell biology going structure by structure: there’s an endoplasmic reticulum for making proteins and moving them, a Golgi for sorting them, vacuoles and lysosomes for storage and digestion, a nucleus for DNA… but it’s perhaps more productive, and less confusing even, to think of the cell as a network of systems (like the human body), the key ones being metabolic pathways, the genome, cell cycle, the membrane trafficking system and the cytoskeleton, with the rest of the cell emerging from them. (this list is by no means meant to be definitive)

Of course, the first eukaryote-like thing, FECA*, presumably emerged from the bacterial realm. Somehow in the interim, between FECA and LECA, our lineage lost many of its bacterial features (such as a murein wall — think Gram staining) and picked up all sorts of eukaryotic traits. One would imagine it not being a case where a single proto-eukaryote population just sits around and gradually eukaryifies until it becomes LECA and then explodes into a ton of supergroups — the pre-LECA eukaryotes were probably diverse and had numerous long-lost offshoots. But somehow, it appears that only one lineage survived to rapidly diversify into modern extant eukaryotes. What where those enigmatic lost eukaryotes? Why did only one lineage survive to bind them all in mystery?

* We could call it them the Lost Eukaryotic Common Ancestors, but the acronym would be confusing…

Unfortunately, where we have a sample size of one in the form of a single phylogenetic event, we are left with little else but mere speculation (the question of the origin of sex falls under the same category). We might be tempted to think the presence of a mitochondrion or its relics in every known eukaryote may allude to mitochondrial symbiosis doing something important. Perhaps a massive selective sweep because this new organelle was that damn awesome. While this may sound reasonable, we have no clear evidence pointing either way. If we knew roughly when eukaryotes arose, we could speculate on some massive environmental change, perhaps a mass extinction where just by chance a single lineage survived. But our estimates for the origin of eukaryotes range from 0.8-3.5 billion years ago, in the wildest estimates. The likeliest time period in my irrelevant opinion, based on fossils and molecular clocks, would be the early Mesoproterozoic or the late Paleoproterozoic (~1.2-1.8 billion years) — a time period still poorly understood. Hell, at times we can hardly tell whether a microfossil is even biotic in origin, let alone discern what made it!

I have probably convinced you by now that both the question of how cells evolve and the issue of the very origin of eukaryotes are thoroughly impossible to address. Usually when people write about science, the story works towards gradually clarifying one conundrum or another. Yes, there is often the occasional setback and an annoyingly unfitting data point that rudely asserts its foul presence in the midst of your otherwise beautiful hypothesis. But the topic of eukaryotic evolution is a whole other type of story — in fact, while the protistan phylogeny has been clearing up over the past decade, the question of how they got there in the first place slipped further and further away. And the recent adventures in protistan genomes and proteomes only make it worse — by rendering the Last Eukaryotic Common Ancestor unbearably complex.

But there is hope, and it lies in the bewildering diversity of eukaryotic cells — as protists. We can still learn how eukaryotic cells evolve, and work on those general principles and models that are the holy grail of evolutionary biology (as much as anything can be holy in science, but we try!). We could perhaps even extrapolate those principles back in time and use the few subtle clues we have to uncover some of the FECA’s descendents’ path to eukaryocy (fine, eukaryote-hood). In fact, in the next post we’ll look at once such case in the evolution of membrane trafficking machinery. We still have a vastness of post-LECA diversity and evolution to address.

Anywhere there is heritable diversity, there is an evolutionary system awaiting attention. Like culture and language, cells are no exception.

*Actually it’s mostly forested hills around here with the occasional patch of corn and soybeans, but we can’t let “facts” interfere with our stereotyping…

Cornfields! All there is in Indiana... don't let the camera lens fool you!

This means the only marine protists I’ll be able to play with for the next little are fossilised forams (of which much of this town happens to be built), but fear not — we’ve got plenty of freshwater and terrestrial critters to sample around here. Furthermore, I’ve got my hands on more Paramecium (a ciliate) stocks than one could ever dream of. Among them, KILLER Paramecia! I’ll explain what they are in a later post, but let’s just say they involve everything from violent murder to viruses, bacteria and mysterious coiled ribbons of unknown origin. Many of these Paramecium stocks are quite old and have historic value, being direct descendants of this very department’s Tracy Sonneborn, notable for his work on epigenetic inheritance of cilia patterning, as well as discovering the killers and much outstanding Paramecium genetics work. For the speciation aficionados among you, the Paramecium aurelia species complex is a messy tale of multiple genome duplications and complicated sexual relations with love triangles of mating types.

A Paramecium cell with DNA in blue and prey E.coli bacteria in red and green. The big blue blob is the somatic 'macronucleus', the site of transcriptionally-active DNA. The pale blue-staining (artefactually) clumps are waste crystals, while what looks like a bubble of candy is a food vacuole full of freshly swallowed bacteria. (63x oil, confocal)

Despite being known by many kids in school classrooms, Paramecium is quite a poorly-understood organism — no doubt complicated further by pretty much everything about it being strikingly complicated. Depending on the species, this ciliate can get large for a single cell — up to 350um, or more than a third of a millimetre. It has not one but two types of nuclei, and must have sex every few generations or die. Some species can make do with having sex with themselves, through a process called autogamy — induced by starvation. Surely there must be a lesson in there somewhere for when life gets tough and suitable companions few and far between… but I digress. One species of Paramecium farms algal livestock inside it, while others largely subsist on devouring bacteria and whatever small flagellate is foolish enough to get in their way. You can see a video of the feeding process in action here. Just for fun, on the right is a micrograph we got while being trained on the confocal (there will surely be plenty more to follow over the months, or years): we have been feeding Paramecium shiny coloured bacteria to be able to track prey through their ‘digestive tract’. The result was pretty and quite dazzling to the non-microscopists in the lab, much to our satisfaction…

Another component of what I do here is perhaps a bit less scenic. Every scientist must pass through a ruthless test of one’s endurance (or two, or many, many… many), and a perfect task to satisfy that is a mutation accumulation experiment. In a nutshell, you start with a bunch of clonal lines and allow them to accumulate mutations while minimising the effects of selection. You can reduce the relative force of selection by decreasing the population size. You may have heard of some additional threats inflicted upon endangered species simply due to them being small in number — not only is their gene pool impoverished (thereby making them vulnerable to change), but bad mutations begin to accumulate thanks to genetic drift. Essentially, we raise our organisms as ‘endangered species’ (while keeping the environment constant) by keeping their populations low and constantly bottlenecking them as often as we can, by randomly picking a single individual to go on to the next generation.

As you may begin to gather, when such an experiment works well, it really doesn’t — your lines start dying off left, right and centre due to deleterious mutations. Ideally, if anything survives the 2000-4000 generations you’re forced to watch them through (and some better make it, else angry PI and no funding =( ), a several genomes get sequenced and you not only get an honest, accurate measurement of the mutation rate, but a sampling of the mutational spectrum freed from (most) selection. What’s amazing is that even in the near-absense of selection (save for purifying selection of lethal mutations), you end up with drastic phenotypic changes rather quickly. While selection and adaptation have hoarded most of the attention in evolutionary biology, non-adaptive (and non-selective) forces like mutation (including mutational bias) and drift too play quite a major role in evolution. While mutation accumulation experiments are hard, frustrating work, they provide important data for grappling with evolution’s very principles. But do appreciate that behind some modest numbers lie many grueling years of work and a sea of graduate student tears (and those of postdocs, RAs, technicians…)

By the way, this means that if anyone claims evolution can’t be demonstrated in the lab… I can personally veto that, kthx.

Lastly, just for fun, my friends and I have taken the rocky road to time travel — or digging around in Indiana’s many fossil strata and remnants of a long-lost sea. There is something truly surreal about picking up corals and brachiopods in southern Indiana. Something is likewise surreal about driving past a giant billboard for the Kentucky creation museum en route to said fossils.

Ordovician (~520 million year old) fossils from southeastern Indiana! The tusk-like things are giant horn corals, and the rest are brachiopod shells, bits and pieces of trilobites, and corals. In the matrix around them is probably loads of ancient protist microfossils, but those take skill to extract.

Adorable trilobite, partially rolled-up...for over half a billion years. By the way, these things apparently don't come pre-cleaned like the ones in museums. Actually, pretty sure the museum ones didn't come cleaned, assembled and coated either...

Nematodinium, a Warnowiid dinoflagellate with an ocelloid (left, double arrowhead) - the subcellular camera eye structure this blog is named after. Note the nematocysts (micro 'harpoons') indicated in the right image. (Hoppenrath et al. 2009 BMC Evol Biol)

We’ll start off in the shallow seas, amongst the kelp forests – I’d like to point out that not all protists are microscopic, and some, like the multicellular brown alga Macrocystis (Giant Kelp) can reach ~50m in length. These enormous protists provide a unique habitat for fishes, invertebrates and fellow protists alike. The sleek blades of the seaweed are covered in tiny houses of the bryozoans, which themselves likely host a microcosm of unique microbial diversity. An occasional labyrinthulid – a distant member of the same supergroup as the kelp – may form an elaborate network of amoebal traffic jams. Upon closer examination, the kelp forest is much like the Amazon rainforest, teeming with epiphytes and various attached animal, protist and bacterial communities and an entire ecosystem built upon them.

Gromia, a filose amoeba notable for being large enough to leave tracks on the ocean floor. (Burki et al. 2002 Protist)

We look towards the powerful holdfast (‘root’) of a nearby kelp giant. On it crawls a fine-footed amoeba with a colourful test – Gromia, who made it into the news a couple years ago for being large and heavy enough to leave tracks in fine sediments, an ability previously thought to be restricted to bilaterian animals. Gromia’s test (‘shell’) has an elaborate opening that can close shut upon retracting the pseudopodia (‘feet’). One interesting feature of these organisms is that they store their waste products inside their test. Upon reaching full maturity, the organism reproduces and forms multitudes of swarmers and abandons the test anyway, so lack of waste secretion is not too much of a problem. In fact, in somewhat close-ish relatives, the foraminiferan Xenophyophores, the stercomata serve a structural role. In other words, storing waste can also provide support and allow cells to grow very big – I’d imagine in some cases, pathological hoarding in humans may also lead to strengthening their houses, but probably very rarely.

As we look down on the ocean floor, we see more filose (“thin-footed”) amoebae: this time carrying enormous elaborate shell structures full of chambers, windows and canals connecting them. You see buried in the sand the abandoned ruins of these architectural marvels – thousands of empty foraminiferan shells strewn across the ocean depths, many fated to persist through eons in limestone. Foraminiferan size and preservation potential led to them being arguably the first protists mentioned in human history – enormous fossil numulites, centimetres in diameter, are embedded in the limestone used in ancient Egyptian pyramids, taking on a second life as part of enormous and everlasting structures of the human realm. You can take a look at some photos of Egyptian nummulites in situ (site in French). Here’s a mini-blog of a paleontology trip (in English) to Egypt starring loads of adorable foram disks. Keep in mind that these are all single-celled organisms (probably with a single nucleus), so reaching sizes in centimetres is quite impressive for these guys!

Large forams are far from extinct, however, and the living UFO-shaped condos we see in these shallow waters are actually tropical Marginopora – I’m calling them condominiums because they house multitudes of symbiotic algal tenants – more dinoflagellates. While the motive beyond hosting algae is far from altruistic and is perhaps more closely analogous to farming,  it’s difficult not to fall for some anthropomorphising when the forams feature window-like openings for the captive algae. In some forams, the tests also possess little alcoves for the algae – whether these alcoves are there specifically for the algae or the latter just happen to like hanging out there remains to be properly investigated, but the architectural complexity of these creatures is remarkable nevertheless. For more images and descriptions of some of the foraminiferan structural marvels you can check out this illustrated glossary site featuring Hottinger’s amazing SEMs and diagrams.

Numerous live Marginopora forams. Each is probably about a centimeter in diameter, for an approximation of scale. (Source)

We could get stuck poking at forams for many hours, but we need to move on. We will definitely come back to these awesome amoebae, partly because they’re one of my favourite protist groups. Up next we’ll take a look at the close relatives of some foram symbionts – the dinoflagellates. Dinoflagellates, or dinos for short, are a diverse group of whirling single-celled organisms carrying a characteristic flagellum wrapped around their waists. They can be predatory, photosynthetic or both, and some groups feature incredible parasites. Some dinos have a habit of gobbling up toxic bacteria and inadvertently concentrating them (and their toxins) as they bloom. The seafood industry has a less-than-amicable outlook on these creatures for that reason. Dinos, among some other algae, are often responsible for bans on shellfish gathering you may see in coastal areas. But they’re not all evil to us – our seeing eye dino, Nematodinium, is a high level predator that is relatively rare – so rare that none have yet been cultured, and very few people have ever seen these remarkable organisms. One must sift through cubic metres(!) of seawater using a microscope in order to spot just one or two. Unfortunately, this poses a great barrier to understanding what the ocelloid actually does and how it works.

Karenia, a photosynthetic dinoflagellate with a tertiary endosymbiont (Andersen & Patterson via ToLWeb)

If you look at the first image in this blog, you may wonder whether the nucleus, indicated by ‘n’, can really be that big. Oh, it is. Dinos have some of the largest eukaryotic genomes, and that’s just the beginning of their strangeness. You may notice something chromosome-like about the nuclear texture – dinoflagellates have massive condensed chromosomes visible without staining. They also lack a few histones – proteins used for wrapping DNA around them in sane eukaryotic nuclei. The massive genomes are full of junk, some of which may perhaps now have taken on a secondary structural role. Furthermore, every gene transcript made by the nucleus has a special starter “splice leader” sequence attached to the beginning of it. The nuclear genomes aren’t the only messed up compartment – mitochondria contain short linear gene fragments with only three coding genes and ribosomal DNA (which is responsible the RNA part of ribosomes), the later fragmented all over the place. The plastid genomes, on the other hand, are full of small circles containing a single gene each, and get transcribed into repeating linear sequences much like a cylindrical stamp works.

On the topic of weird doughnut-shaped DNA genomes, there’s an ever-ubiquitous Bodonid swirling about in the distance. Let’s head over there. We see a small flagellate crawling about with a flagellum trailing along the surface of a decaying seaweed, nibbling on bacteria here and there. Since our eyes don’t work on that scale, we can ignore physics and pretend we can sort of see through the cell (you probably would be able to, hypothetically-speaking, but I’m not sure…). Beside the nucleus you see another visible clump of DNA in a thick ‘hockey puck’ shape, and may be surprised to learn that’s a mitochondrial genome – one of the easiest to see with light microscopy.

But that’s just the beginning of the weirdness: the path of genetic information from DNA to protein involves an unusually high intensity of RNA-editing, or sequence modification in messenger RNAs after being transcribed from DNA. The templates for sequence correction come from multitudes of small circles of DNA. When researchers first started sequencing mitochondrial DNA from these bugs, they were shocked to see total nonsense where highly-conserved genes were supposed to be. Later it was revealed that an elaborate process involving a few hundred proteins was required to fix those nonsense sequences to code properly. This topic deserves a post of its own, but for now here’s a final neat tidbit: this bodonid’s close relatives, Trypanosomes – some responsible for African Sleeping Sickness, Chaga’s disease and nagana,  a major reason raising cattle is so damn difficult in Africa – have elaborate meshes of interlinked DNA circles in their mitochondrial genomes, woven together much like chainmail. Oh, and this clump of DNA somehow manages to rotate during replication, because it’s just not weird enough otherwise. (I have some ramblings on these weird mitochondrial genomes towards the end of this post here.)

Perkinsella endosymbiont in Neoparamoeba. n - nucleus; k - kinetoplast (disk of mitochondrial DNA); NN - host (amoeba) nucleus. Transmission electron microscopy. (Dykova et al. 2003 Eur J Protistol)

One such critter with a messed up mitochondrial DNA disk, Perkinsella, has found a home in an amoeba (Neoparamoeba), and the relationship is so intimate that the endosymbiont was initially thought to be a full-fledged organelle. Its role there is far from understood, but neither the host nor the endosymbiont can live without each other. Which leads us to the next point: intimate relationships between different species, symbioses (this includes everything from parasitism to mutualism), occur fairly frequently in the microbial world and feature some outright bizarre associations. Particularly common are associations between bacteria and protists, where we will begin in Part II.

In the next few ‘microdives’ into the protist world, I would like to systematically destroy as much as possible of what you may have learned about how organisms are supposed to function. Not only are attempts to depict a ‘typical’ eukaryotic cell crude at best, the ‘typical’ cell most often depicted is quite derived and a poor representation for eukaryotes as large. Animal cells have undergone a loss of functions per cell (as there are more cells and cell types), and can hardly live independently. Cells of multicellular organisms are degenerate and fail to capture the true wonder of cell biology. In a similar way, ecology is in some ways more exciting on the microbial, and while many principles are preserved, many new and unusual interactions are introduced at that level.

However, before following an obscure conference, you might find yourself wondering – what are protists in the first place? The intro post gives an overview of their importance and phylogenetic position, but might still be vague on what they are in lay terms, without excessive phylogenies. Or why they’re such a strange group in the first place. This calls for a very brief sketch of some history of the field (that has many fascinating tidbits here and there, which I’ll try to incorporate here and there).

In many societies, if not most, people tend to fundamentally classify the living world into things that move and those that don’t. Things that move are roughly ‘animals’, things that stand around are ‘plants’. The latter also tend to be green, making things quite convenient. Mushrooms, due to not being green and tasting very differently, are weird plants. For most of our existence, this system worked perfectly fine, and still does for most people. Few are foolish enough to venture further.

Things got a little confusing when van Leeuwenhoek devised his own microscope design (single spherical glass lens) and fathered microbiology with it. He looked at pond water, among other things (notoriously, including his own feces) and discovered a whole new world of things that in some very loose ways resembled normal ‘terrestrial’ life, but were still unbelievable. Prior to van Leeuwenhoek’s discoveries, a life as a single cell was inconceivable (of course, few knew about cells at that point either). The microbes were called “animalcules”, a cute-sounding name itself based on the plant-animal dichotomy. The motile and predatory microbes like ciliates were deemed to be clearly animals, while the green sessile creatures were micro-plants. Of course, things get funny when you run into the swaths of algal diversity that are flagellated and very motile, and often predatory. Things get funnier yet when you have weird secondary and tertiary acquisitions (endosymbioses) of photosynthesis, and phenomena like chloroplast (plastid) theft. But they didn’t know that yet. All they saw was a world for which there was no folk biological prerequisite. Our folk biology is exclusively macrobial.

Interestingly, this taxonomic mess persists to this day in the naming system of eukaryotes. We have two nomenclature codes – one for botany (ICBN) – including fungi – and another for zoology (ICZN). While most taxonomists are (or should be) aware of the vast world outside plants and animals, this strong relic of our folk biology persists to this day, resulting in total chaos with groups like Euglenids – clearly motile and often predatory, but many members very green and algal in the meantime. Yes, this means Euglenid taxonomy falls under BOTH codes, leading to sets of two slightly different names and ranks for each taxon. We like to think of modern science as this super objective activity devoid of historical contingency and human factors, as something that transcends cultural backgrounds. Yes, the scientific method is wonderful, probably the best system for gradually acquiring higher and higher accuracy of predictions, but I like to point out from time to time that science remains (and always will be) a human activity, with all the quirks that come along with that.

I digress. A century and a bit after van Leeuwenhoek’s work came Haeckel, and established the kingdom Protista. By then it was becoming clear that the plant-animal dichotomy does not work, nor does the plant-animal-fungal system that came after (of which we still see relics everywhere). The microbes were clearly a separate ‘thing’ taxonomically, or in other words, things make a lot more sense if you treat them as such. Protista was a kingdom for creatures that defied the animal-plant-fungal classification, which remains the case to this day. Of course, the boundaries and definitions are sometimes vague and disputable, as expected of a group that is defined by exclusion. But apart from the clear distinction between prokaryotic and eukaryotic microbes that arose with the sophistication of ultrastructure (fine cell structure) studies, the kingdoms remain the same to this day.

What is somewhat worrisome to me is the ever-growing gap between the contemporary work of the phylogenetics community (researchers who look at evolutionary relationships between organisms) and the worldview of those outside the field, including that of other scientists. While one small group — many of whom are at this conference right now — is developing a more and more accurate and sophisticated picture of microbial relationships, the rest of the world still lives in Haeckel’s time at best.

Curiously, you may have noticed above that at this conference we have two societies meeting – the protistologists and the phycologists. You may perhaps recall from the tree and brief discussion in the introductory post before that algae are…protists. So why two societies, especially since the phycologists are, by defintion, a subset of protistologists who study photosynthesising things (especially macroscopic photosynthesising things like seaweeds). ISOP (Int’l Soc of Protistologists) actually used to stand for Int’l Soc of Protozoologists – yes, protozoology as the counterpart to phycology (study of ‘protophytes’). The deep folk biological split between non-motile green things and motile non-green things persists even in the organisation of our scientific societies and conferences full of experts who definitely know better. Tradition is strong, and science is still a human activity.

So I hope this clears up a bit on at least why there’s a total clusterfuck regarding the term ‘protist’. To make things better, we don’t have a total consensus on a definition of ‘protist’ even in the field. I use the word differently from other people here. Some people exclude macrobial (large) things, some exclude green and red algae as well, etc. My definition — the one that really matters since I run the show here — is that a protist is anything that is a) eukaryotic; and b) not an animal (defined by shared origin of multicellularity, including sponges of course), land plant (embryophytes – green ‘algae’ that produce some sort of embryo tissue and are largely terrestrial) or fungus (defined by…let’s not go there today, but roughly speaking, chitinous walls and presence of a dikaryotic life cycle stage, which I believe is in at least most of them). Later we can talk about phylogenetic vs. taxonomic definitions, paraphyletic groups, etc. But for now, have a random video of an amazing pseudopodial network of a naked freshwater foraminiferan: (description in YouTube link)

Will definitely explain this organism a lot more later, but keep in mind that this video is in real time, and the movement of particles in that pseudopodial network is unusually fast for a cell. Foraminiferans have a trick for this, and it’s really incredible for anyone interested in how cells work. As an aside, some of these buggers can hold down a small animal (eg copepod, brine shrimp) and devour it from within. So much for the common sense idea that multicellular things eat unicellular things, no exceptions.

I will get back soon, with lots and lots of goodies from this protistology conference, which is so far absolutely amazing. As obscure as our field may seem, there are at least a couple hundred of us in it – almost a crowd, if you will. It is wonderful to be around people who share you interests, but even more so when your interests are so odd and arcane.

Until next time (where I will produce a proper post with pictures and references). For now, feel free to follow the conference twitter feed!

Nearly everyone finds wonder in at least some aspects of natural diversity — whether it lies in the appreciation of exotic plants, the variety of domesticated breeds or simply enjoying a day off from urban chaos. From colorful venomous frogs to fluffy pandas or the strange terror of deep sea fishes, we are all familiar with the iconic images of our biosphere’s diversity. But the greatest biodiversity lies in the unseen, a world so alien yet so pervasive around us. Microbes, not macrobes, comprise the overwhelming majority of the earth’s biosphere, in quantity, mass and variety. While bacterial microbes are quite familiar to the microbiologist and anyone keen on the study of diseases, much less commonly spoken of are the microbial eukaryotes (and related macroscopic offshoots that are neither plant, fungal nor animal) — the protists:

Overview of eukaryotic diversity - note the paucity of non-protists.

(modified from this Tree of Eukaryotes)

Protists can be found practically anywhere. One is likely familiar with green ‘pond scum’ that blankets pools of stagnant water in the summer months. This was my first introduction to microbial life in my childhood, when a simple microscope revealed an entirely alien world perfectly accessible on earth. Those who live by the sea need not go even that far – the seaweeds lining the ocean shores are themselves protists, having acquired multicellularity entirely independently of animals and land plants. However, most members of the kingdom are microbial, and among them are the more surprising forms. One of the strangest among them is a single-celled alga bearing a complex camera eye, complete with analogues of a lens, an iris and a retinoid. This structure is called the ocelloid. It is not clear how the organism uses the potential image from this contraption, for it has neither a brain nor any neural system at all. Imagine being able to see the world through its eyes, a world in microns, dominated by a different set of physical principles!

While we cannot even obtain this wonderful creature in culture, we can at least fantasize about its life and that of its brethren. Our fantasies shall remain rooted in the observed reality as much as possible, since it is too easy to lose footing and get lost in a realm so different from ours. That said, there is plenty of room for imagination and somewhat aimless recreational hypothesizing, so from time to time I intend to include some sketches (doodles like some here) and stories.

Closely looming over the appreciation of life’s diversity lies the question of how it came to be – in other words, evolution. In addition to exploring the variety of ways protists can be expressed and how they ‘work’, I am interested in general evolutionary mechanisms. After a while, simply looking is no longer enough. While most are at least somewhat familiar with the mechanisms of adaptation and selection in evolution (often synonimised with the term, albeit quite erroneously), there are other crucial mechanisms involved, such as drift and mutational bias. Those topics tend to be excluded from popular literature, perhaps due to their traditionally technical approach. I think a scientific approach to evolution does have its place in popular science, and hope to bring some of it to light in a hopefully somewhat accessible form.

Now, about the macrobe in question: I am currently finishing up my undergraduate at the University of British Columbia and will stay at the bench during my year off before grad school. I have been blogging about protists and evolution at Skeptic Wonder, where I will continue blogging but in a more technical and loosely organised manner. I can be found and poked on Twitter via @PsiWavefunction;  and reached by email at psi.wavefunction [at] gmail{dot}com. I am also a moderator on the microscopy subreddit, a community for sharing micrographs and discussing our adventures in the world of the small. Questions about identification are particularly welcome there, so come along and join us!

My past writing at Skeptic Wonder has focused largely on protists, perhaps unsurprisingly — posts have included things like the complex armoured cell surface structure of cryptomonads and specialised plastid-thieving ciliates. Bouts of procrastination with a microscope have yielded piles of pictures and videos of glimpses at microbial life presented as “Microforays“. Broader topics include a few posts on non-adaptive evolution: including an overview of Constructive Neutral Evolution and an attempted explanation of a recent paper on protein complexity evolution. Occasionally I do warily peek outside the protist kingdom, which has led to posts on other strange creatures like social onychophorans and extremely salty square archaeans.