Nov 292013

As I was saying, we vertebrates tend to have a high opinion of the big clump of neurons that sits at one end of our spinal cord.  And so we should: in creatures like us, that’s where the magic happens.  The bigger the clump, the more cognitively versatile the organism; remove it, and the whole organism comes to a stop (though it may run around for a while, first).

But, as we know, even unicellular beings are capable of sensation and coordinated movement, and can show complex, even purposeful, behaviours.  So, it was probably inevitable that some well-meaning scientist would try to equip them with a central nervous system of their own.

Stylonychia crawling Actinophrys

Stylonychia mytilus crawling on a filament of algae. Image by Actinophrys, on Flickr. Click for Link.

In 1880, a German researcher named Th. W. Engelmann undertook a close inspection of the tissues of the ciliate Stylonychia mytilus.  Like other members of the ciliate group loosely known as “hypotrichs,” Stylonychia has, on its “belly,” a crop of thick, mobile cirri: bundles of fused cilia that it uses like little legs, as it scrambles around on solid objects in its sunken world.  These pseudo-legs work very well, and a crawling hypotrich can look a lot like a beetle or cockroach.

Unlike the limbs of insects, the cirri of hypotrichs lack conspicuous attachments, such as muscles, tendons and nerves. However, looking very closely at stained samples, Engelmann was able to detect, at the bases of Stylonychia’s cirri, groups of fibres which he called “Wimperwurzeln,” or “ciliary rootlets.” These fibres, he speculated, might just function as nerves do in “higher” organisms, serving as the conductive tracks along which the stimuli that move the cilia might move!

It was an innovative idea; however, it did not spark much excitement. Despite his impressively clear record of these small structures, the suggestion that he had discovered animal-like organs in unicellular creatures might have come at the wrong time. By 1880, the view of protozoa as miniature animals, bearing a complete set of reproductive and alimentary organs, had been discredited a long time before. In the late 19th century, protozoa were conventionally seen as primitive organisms, little more than bags of the all-purpose protoplasm that constituted, in Thomas Huxley’s memorable phrase, the “physical basis of life.”

But times change, and the idea that free-living cells might be composed of differentiated tissues would came back into style (in fact, in the early 20th century some protozoologists completely rejected the cellular nature of their organisms).

Charles Kofoid picture

Charles Atwood Kofoid

In 1914, Robert G. Sharp–working in California under the guidance of the eminent protozoologist Charles Atwood Kofoid–published a paper in which he boldly claimed to have found a ciliate that not only had nerve-fibres, but a full-blown centrally located “neuromotor apparatus.” He discovered this structure in an organism called Diplodinium ecaudatum (now known as Epidinium ecaudatum), a symbiont in the stomachs of cattle. What Sharp found had never been recorded anywhere: a small mass of fibres close to the cell’s motile organelles, and serving as “the common center of motor influences.” He had discovered the organ that controlled and coordinated the moving parts of the ciliate, in effect, the cytoplasmic “brain” of the cell. He called this the “motorium.”

Sharp’s paper kicked up a little whirlwind of scientific activity, particularly among his colleagues at Kofoid’s laboratory. The following year, Kofoid himself described a “neuromotor apparatus” in the intestinal parasite, Giardia. Shortly after, Harry B. Yocom, another worker in Kofoid’s group, published the discovery of a full-blown neuromotorium in the hypotrich Euplotes patella (a “walking ciliate” like Stylonychia).

But why ascribe a neural function to the structures he saw in Euplotes? Yocom goes into some detail about that. In the first place, these fibres turn a vivid red in the fuchsin from Mallory’s stain, just as nerve cells do in metazoa; in the second place, he explains, these fibres are found in association with the moving parts of the ciliate: the oral membranelles and the locomotory cirri.

Yocom Euplotes neuromotor apparatus circled in red

Yocom’s illustration of the neuromotor apparatus in Euplotes patella, with the “motorium” circled in red.

Finally, the behaviour of Euplotes patella appeared to support this interpretation. It is, perhaps, a classic example of hypothesis leading observation by the nose. To Yocom, it seemed evident that E. patella was using its “anterior lip” (the bulge at the top of the cell, which showed a red-staining lattice of fibres) as a sensory organ. What’s more, the transverse cirri, which were linked to the “motorium,” moved in a coordinated way, while the unattached cirri moved randomly.  As Yocom puts it: “[T]he whirling irregular movements of the frontal ventral and marginal cirri are in no way coordinated with the regular rhythmical movements of the membranelles or with the backward kick of the cirri.”

Or, so it looked to him.

Up to that point, the function of the “neuromotorium” as a “coordinating center” for the cell’s movements was simply a hypothesis, unsupported by experiment. But confirmation was not long in coming. In 1919, C. V. Taylor–yet another worker from the Berkeley circle–conducted an experiment on Euplotes patella, the ciliate Yocom had studied in such detail the year before. Using quartz microscalpels, he severed the fibres running between the motorium and the anal cirri (the prominent group of five heavy cirri in the posterior half of the cell, now usually known as “transverse cirri”). The experiment resoundingly confirmed the hypothesis; detached from the motorium, the cirri did not seem to work properly at all: “Severing the fibers to the anal cirri affects both creeping and swimming…Destroying the motorium or cutting its attached fibers interrupts coordination in the movements of the adoral membranelles and anal cirri.”  (Taylor, 1919)

Paramecium nerve center with red circle

Paramecium from Rees (1920), showing a tracery of fine “neurofibrils” (skeletal microtubules, presumably) converging on the “nerve center” of the cell, circled here in red.

From then on, the neuromotor apparatus turned up in one ciliate after another. It was found in Paramecium (1920), Balantidium (1922), Tintinnopsis (1926), Dileptus (1927), Chlamydodon (1928), Uroleptus (1930), and Oxytricha (1935). Along the way, doubt steadily faded, and by 1927 it was possible to affirm plainly that “a complicated neuromotor system has been conclusively demonstrated to exist in certain ciliated infusoria.” (Visscher, 1927) It had become, in North America, at least, a solid fact.

But even solid facts can turn fluid again, and then evaporate like the canals of Mars.  It can happen slowly, or all at once.  Sometimes a hypothesis dies a quick death, when an experiment disproves it; sometimes it is swept off in the riptide of a better theory; and sometimes it just get nibbled away, while the world slowly changes around it, until one day nobody can remember why it had ever seemed true.

The neuromotor concept had a long run, outlasting Kofoid himself by a decade and a half.  Even the advent of electron microscopy did not kill it off, right away.  As late as 1957, EM seemed to reveal in Euplotes “a mass of intertwining rootlet filaments” corresponding to the neuromotorium, as well as a whole system of intracellular fibres which were mainly dedicated, as the authors argued, to “the coordination of the ciliary beat.” (Roth, 1957) But when R. Gliddon again placed Euplotes under the electron microscope, in 1966, he could not find anything you could call a motorium.  It had disappeared.

In that same year, two researchers in Japan finally got around to replicating Taylor’s classic experiment on E. patella–the experiment that, arguably, had kicked off the neuromotorium gold rush. (Okajima and Kinosita, 1966) But now, the results were very different.  The investigators severed the “neurofibrils,” just as Taylor had done, and captured the ciliary movements on film; however, this time the cirri just kept on moving in their usual coordinated way, as if nothing had happened. It is not known why Taylor’s Euplotes had behaved differently.  Possibly, he mangled the poor things while dissecting their “neurofibrils” and made his celebrated observations on organisms in their death throes.

In 1970, Dorothy Pitelka was ready to call the game, announcing the general “abandonment of the old concept of a fibrillar neuromotor system in ciliates.” A casual search in Google Books turns up one last, brief reference to the “neural fibrils” of Paramecium, in a high school biology textbook published in 1983.  After that, nothing.

So what were the “neurofibrils,” in the end? They were not a product of poor equipment or fanciful observation, but rather the opposite. Remarkably, it seems that microscopists of the day were already detecting parts of the cytoskeleton–the scaffolding of microtubules and filaments that give the cell its shape–as well as the pellicular “latticework,” the so-called ciliate “silverline system” which would later be fully exposed in silver nitrate and protargol preparations. Interpretation lagged behind observation for a generation or two. Seeing had outstripped understanding; then new information came, and the old certainties just sank back into the pondwater.

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Nov 232013

When René Descartes searched through the human brain to find the Seat of the Soul, he settled on the pineal gland, a small endocrine organ found in nearly all vertebrates. It seemed like a good candidate, because it is a singular organ, not duplicated on each half of the brain but perched right on the midline, where it could, as Descartes imagined, receive sensory impressions through little pipes, and flex the muscles of the body by exhaling “animal spirits” along a system of hoses leading to the arms and legs.

Descartes brain 4b

Illustration from Traité de l’Homme (1644), showing the teardrop-shaped pineal gland perched in the skull like a little Mecha-pilot.

Descartes’ soul sits at the control centre of the meat-puppet, gathering news of the world through its eyes, ears and nose and exerting its will upon the world through the pneumatic machinery of the body.

It is easy to recognize in his conception a structure analogous to  what we know as the nervous system. We no longer think in terms of “animal spirits,” but rather of “neural signals,” and we no longer place the mind within any particular gland in the brain. But for most of us, who have only a rough understanding of how it all works, this “signal/transmitter/receiver” scheme is only another metaphor, just a little more sophisticated than the one Descartes used. By and large, we are still operating with the notion of an insubstantial mind somehow localized within a “central” nervous system, conducting its business with the world through an extensive network of  bodily filaments.

Indeed, many of us find it hard to even conceive of an intelligence which is not concentrated  at the top of a hierarchy, running from the brain (where the cogitating self resides) to the tips of the peripheral nerves, where the world lies waiting to be felt, heard and seen.

So, the distributed intelligence of the octopus nervous system–half of its neurons are in its arms!--strikes us as something bizarre and wondrous, requiring further exploration and explanation. Challenging the naive expectation that cognitive processing should be “central” and the organs of sensation “peripheral,” the octopus researchers have devised ingenious experiments to show that the arms of the mollusc continue to perform goal-oriented behaviours, like prey-seeking, exploration and danger-avoidance even when they are severed from the so-called brain.

And if it seems marvelous that a detached octopus arm can still sense and react  to perceived danger, how much weirder is it that a single cell can do all these things, without the benefit of any nervous system at all? But this is perfectly commonplace in the protist world, where one-celled hunters swim around, stalking one-celled victims, who recoil when they sense trouble, take shelter in their shells, or hide from their enemies in clumps of debris.

Just imagine if a single cell of your body could cut loose and go wandering about under its own power like that, hunting and consuming prey! Oh, right…they do. In fact, it is perfectly ordinary for eukaryote cells, whether they are inside larger organisms or roaming at large in the “world,” to exhibit complex behaviours that may be remarkably hard to distinguish from the kinds of behaviours we observe in large, multicellular animals.

Take a ciliate like Stichotricha aculeata. It usually inhabits a shabby, homemade tubular dwelling (a lorica), made up of mucus mingled with debris. It lives by brushing smaller organisms — bacteria and some of the daintier protists — into a mouthlike aperture, where they are packed up in little food-bubbles (vacuoles) and digested. Like a cat or a crayfish, it is both large enough to be a predator, and small enough to be prey. Consequently, it is a cautious creature, relying on its lorica for protection. When it senses trouble, it withdraws into its tube, and when the coast is clear it will put out its long feeding apparatus. Like other ciliates, it can sense movement (probably with the help of sensory cilia, which are common in eukaryotic cells), and is easily startled. If you should tap on the microscope stage with your finger, while you are watching it, it will detect the vibrations and pull back.  After hiding for a while in its jelly-tube, it will extend its proboscis, tentatively. If it encounters no more trouble it will begin to feed again.

However, if the disruption is sufficiently violent or prolonged, it may abandon its lorica altogether, as the closely-related Chaetospira does in a video I recorded last year. The Stichotricha in the embedded footage which follows has already fled its original “home,” and taken shelter in a little enclosed space, between the coral-like tubular dwelling of a colonial flagellate called Rhipidodendron huxleyi, and a mucoid colony of some other organism (Spongomonas?). In this makeshift lorica-substitute, it is behaving exactly as it normally does when at home, sliding forward and back, feeding, withdrawing, advancing, always hungry, and always vigilant:

It is easy to see why early microscopists referred to these creatures as “animalcules: “very small animals”. Without a nervous system, ciliates like Stichotricha and Chaetospira exhibit behaviours strikingly reminiscent of a fish lurking in a crevice, or a case-dwelling insect, like the larval caddisfly. If they often remind us of “true” animals, it is well to remind ourselves that, after all, they have a way of life that differs very little that of other cavity-dwelling aquatic creatures, like the ones we might find on a coral reef, or like this larval midge, in the gravel of a freshwater stream:


Nov 222013

Stewart Brand usually gets credit for the quote, but apparently it was Craig Venter who said it: “If you don’t like bacteria, you’re on the wrong planet.  This is the planet of the bacteria.”

Actually, the second part of that, the play on Planet of the Apes, was probably lifted from the title of an article by Stephen Jay Gould, included in his book Full House.  When I was asked to review the book, eighteen years ago, one passage blew a hole in my world view: “We live now in the ‘Age of Bacteria.’ Our planet has always been in the ‘Age of Bacteria,’ ever since the first fossils—bacteria, of course—were entombed in rocks more than 3 billion years ago.”

It’s funny that it was Stephen Jay Gould who steered me away from my zoocentricity, because the preeminent explainer of evolutionary biology rarely had much to say about microbes. Pulling one of his books off the shelf and scanning for organism names in the index, I see: ammonites, aphid, angler fish, Archaopteryx, asses, Australopithecus–ah, there’s “bacteria,” with two brief entries–and then, bees, birds, Blatella germanica (a cockroach), blue-footed boobies, boobies again, then brown boobies, brown hyenas, coelecanths….and so it continues until we get to Eschirichia coli, and much later, two entries for “prokaryotes.”  That’s it for microbiology in that book (Hen’s Teeth and Horse’s Toes).

Protists don’t rate a single mention. And it is much the same story in Gould’s other works.  Even his desk-bending opus ultimum, The Structure of Evolutionary Theory, mentions “protistans” just a handful of times, mostly in connection with the observation that gradualism will govern the rate of evolutionary change in “asexual” organisms.  (Most protists are as sexy as can be, but let’s leave that aside, for now).

I didn’t bring this up to bash Gould.  He wrote mainly for a general readership, and microbiology wasn’t his thing anyway. But perhaps it reveals something that, as late as 2002,  it was possible to write a 1,400 page treatise on evolutionary theory in which the only source cited on “protistans” is D’Arcy Thompson’s On Growth and Form, published in 1917. And I’m not sure that Gould’s zoocentrism is all that unusual in his field.  Certainly, Lynn Margulis (enthusiastically wrong about some things, but the best friend a microbe ever had) often complained loudly about the dominance of “zoologists who today call themselves ‘evolutionary biologists’.” (Acquiring Genomes, 26) Last year, there was an international congress on evolutionary biology in the big city down the road from my village. Scanning the program, I noticed that most of the talks were centred around macroorganisms of one kind or another (tigers, termites, toadstools, and tumtum trees). A friend who teaches evolutionary biology at CUNY was in town for the event. “Don’t worry,” he teased me, “there’s bound to be one or two people giving talks about the weird stuff!”

As my friend knows quite well, here on the “Planet of the Bacteria,” the “weird stuff” is really creatures like us: great, shambling, genetically-coordinated quasi-colonies, lurching around with more than 37 trillion specialized cells inside them (and hosting perhaps ten times that number of hitchhiker microbes).   The protists seem almost normal, by comparison, though even they are evolutionary oddballs.  All of us eukaryotes are weird, but, some of us are weirder than others.  While plants, fungi and animals make up only a few remote twigs at one end of the eukaryote lineage, the long sideways-projecting stalk on which they sit– comprising what is sometimes called (though I can hardly say it without snickering) “Empire Eukaryota”– is made up mainly of (royal fanfare, please) “Kingdom Protista.”

Needless to say, the natural history of eukaryota was mostly written by protists, and by all rights the study of them ought to be central to evolutionary theory.   Bear in mind that if the original ancestral eukaryote were to emerge from some magic time capsule and land in the petri dish of a modern biologist, it would almost certainly be classified as a protist.   And, if you look closely enough at some of our 37 trillion cells, our kinship with them is hard to miss.  Our lungs and fallopian tubes have genuine cilia that beat just like those of the ciliated protozoa.  Our sperm have flagella (really just another kind of cilium), no different, structurally, from those that power any flagellated protist.  Our bodily fluids are patrolled by ravenous amoeboids that roam around, engulfing bacteria and other other invaders.    Out here in the “Empire” of nucleated cells, protists are us.


Nov 182013

I used to study English Literature.  I did that for a decade and a half, at two universities, and eventually wrote a doctoral thesis on “Postwar American Poetry.”  In all the years I spent researching poetry,  nobody ever asked me why I would want to study something like that.  It’s not that everybody loves poetry. Most people, in my experience, really cherish the time they don’t spend reading poetry. But some people do like it well enough, and we all know that people of that kind are out there, somewhere.

Protists are different.  Apparently, if you happen to be interested in those, you have some explaining to do.  In fact, it’s the first thing most people ask, when I tell them how I’ve been spending my days: Why are you interested in that?

It always deflates me a bit, which is fine, I would not want to be too puffy.  But would they ask me that if I were studying…tigers?


John Goodrich, Tiger Researcher (Image: A. Rybin.  Click to see source)

I’m pretty sure that guy never has to explain why he loves what he does. He catches live tigers in the wild and cuddles their babies!   That’s a solid 40 megafonzies on the Cool-O-meter. But when I mention that I’m interested — very, very interested — in “protists,” I can tell that some people do not necessarily think it is a good thing.

Part of the problem is the word “protist” itself. From a public-relations point of view, it is a mess. First, it sounds too much like a certain other English word. When the subject of protists comes up (as it always does, if I can work it into the conversation) people often mishear me, and think that I like to study and observe “protests.” Which is not so implausible…I’m sure there are “protest watchers” out there, as there are “storm chasers” and “chicken hypnotizers.”   But even when I spell the word out, people over a certain age (my generation, that is)  don’t recognize it anyway. We grew up calling these bugs either “algae” (the placid green ones that remind us of plants) or “protozoa” (the colourless ones that boogie around and try to eat each other, like miniature animals).

These days, the word “protozoa” is being phased out, in professional circles. The reason for this is perfectly sound. It means “first animals,” and protists are not animals of any kind.  The mushrooms in your fridge are more closely related to you (and your dog, and your dog’s fleas), than any of the protists in your koi pond. But although both words were coined in the 19th century, the word “protozoa” is the one that caught on and stuck. In marketing terms, it has good “brand awareness.” So, here we have a field, protozoology, that was already on the margins of the public mind, which now goes by a “new” and unfamiliar name.

And finally, once we’ve established what it is we are talking about, some people still fail to see–amazing as it sounds!–why a person might care about such a thing.  Even biologists, who should know better, tend to think of protists as a weird little sideshow in the circus of life, where the big tent is reserved for elephants, horses and (needless to say) tigers.

I’ll talk about that in my next post, I think.

First, though, since I’ve been belabouring the word “protist,” what exactly do we mean by it?  This blog is about protistology, so there will be ample time to explore that in depth, but a quick working definition might be useful. If I may adapt the excellent and succinct definition offered by Psi Wavefunction, a protist is any organism that is not a bacterium, not a fungus, not a plant, and not an animal. Which means that protistology is, effectively, the study of organisms that nobody else cares about.

Any eukaryote that is not a plant, an animal, or a fungus. – See more at:
Nov 142013

When I was eight years old, I knew what I wanted to be when I grew up.

I wanted to be this guy:

Forty-five years later, I finally look a bit like that. It’s not the wild hair and bulging eyes (which I’ve always had): it’s the glassware. At 53, I finally have an erlenmeyer flask!  I also have a box of pipettes, and a big fat falcon tube filled with a yellow fluid that might well turn into a powerful explosive if I ever let it dry out.  I do not have a brain in a jar, but it’s only a matter of time.

In short: at a fairly late stage of life I am trying to become, in my own small way, a kind of scientist.    I have no scientific training at all.   I am a poet, who happens to have written a bit about protists and microscopy.    I’m hoping this blog will give me a place to write about the slow and sometimes awkward process of learning to think scientifically.

What I’m beginning here could be described as a “citizen science”  blog, but that term doesn’t sit well with my inner eight-year-old.   “Citizen science” is all about “making a contribution,” like those diligent bird-counters, reporting their sightings to the Cornell Lab of Ornithology; or telescope fanciers up till all hours, sifting the barely-perceptible specks from the almost-invisible flecks.   There’s nothing wrong with doing your bit for the cause, but that is not what pulled me into this.  (And really, can you picture a power-hungry “citizen scientist” cackling over a fuming flask?)

Since we do have to distinguish the self-taught amateur from the qualified pro (if only to decide who gets a turn at the electron microscope), I prefer the term “outsider science,” which hints at the kind of not-altogether-healthy obsessiveness that drives a person like me.   Of course, that epithet is, if anything, even less flattering.  While the “citizen scientist” may be, at worst, a gormless do-gooder, the “outsider scientist” appears to be (in the journalistic imagination, at least) a flat-out crank:

(Image: Reidar Hahn, via Symmetry Magazine)

But if the “outsider scientist” is a kook, he is at least a passionate one; and I’m not too proud to admit that something in that picture kind of reminds me of me.

Also, protistology is itself something of an “outsider science,” which has a long history of providing an intellectual home for dedicated autodidacts.  I will talk a bit about that in my next post, or the one after that.