Feb 132015
 

A few years ago, I looked in a sample of water from a bog lake, and saw something like a hyperactive avocado shifting around inside in a tiny kerosene lamp:

The architect of that pretty dwelling is the ciliate Calyptotricha pleuronemoides. The species and genus were discovered in 1882, in samples from a pond near Hertford, England, by an amateur naturalist named Frederick W. Phillips.  Not not much is known about him.  During the 1880s, he was an active member of the Hertfordshire Natural History Society and Field Club, to whom he occasionally read essays on “The Protozoa of Hertfordshire,” based largely on the classification scheme in William Saville Kent’s Manual of the Infusoria.  He was a Fellow of the Linnean Society of London, and he found and named a few new taxa.

In his very first glimpse of the creature, Phillips was lucky enough to catch it in the act of building its lorica. “At first sight,” he writes, “I thought it was an embryonic or encysted stage of some monad; but upon applying a magnifying power of some 900 diameters, I observed that it possessed a singular vibratile membrane, closely resembling that which characterizes the members of the family Pleuronemidae.” A week later, Phillips looked at it again, and discovered that “the lorica had increased in size, and that one end was elongated into a teat-like form.” At this stage, he accidentally allowed the sample to dry out, leaving the organism’s empty, half-finished lorica still attached to a strand of pond-weed. He made a nice drawing of what he’d seen.

Calyptotricha pleuronemoides from Phillips resized

A. First stage B. The same, further developed C. End view of lorica D. The perfect animal E. Ventral view (adapted from Phillips)

To modern readers, accustomed to the impersonal, passive style of scientific writing–“samples were collected,” “living cells were isolated and observed”–there is something pleasingly candid about the way Victorian naturalists report their findings. Phillips doesn’t just describe his new genus, he spins us the tale of its discovery, including the mishap that destroyed his first specimen, and his initial misreading of the oval shell, after which he takes us to the very moment of discovery when he exposed the creature’s true nature by “applying a magnification of 900 diameters.” Something about that reminds me of the exploration literature of the same period. It’s probably not just an accident of style: Victorian microscopists were explorers. Superior lenses and stains had opened up a miniature Dark Continent on their laboratory benches, and a gentleman adventurer from somewhere like Hertfordshire could now penetrate these hidden realms, returning with breathless accounts of what he had seen. A session at the microscope was an expedition into the unknown.

In our time, researchers are expected to pile up some data before going to print, and nobody would attempt to erect a new ciliate genus on the basis of a brief observation of a few specimens. No doubt that is a good thing: the 19th century left a big legacy of poorly defined taxa, many of which are still desperately in need of revision.  But this kind of field work, as sketchy and dilettantish as it might seem now, has largely been put to one side without really being replaced by anything better.  Outside of a few centers of activity, ciliate field work has slowed to a crawl.  Consider the fact that 132 years after Phillips wrote his three-page note on Calyptotricha pleuronemoides it is still one of only two substantial treatments of the species, and the only source that describes the construction of its curious lorica.  Anyone who wants to know more about this ciliate than its name, has to travel back to the 19th century.

poke bonnet

A straw poke-bonnet, from the early 19th century. (Click for source)

Needless to say, the old information is not always reliable.

Phillips perceived immediately, and rightly, that Calyptotricha is closely related to the more common ciliate Pleuronema. Like its cousin, it is equipped with a large, billowing membrane that runs along the right side of its oral aperture. However, Phillips badly misunderstood the shape of this structure, describing it as “a membranous trap, or velum, which in form resembled the old-fashioned poke-bonnet.”

When I first read that passage, the comparison to a “poke-bonnet” confused me. The undulating membrane of pleuronematid ciliates is shaped something like a sail, or a flag: a sheet of fused cilia running along one side of the organism’s mouth. Phillips, however, interpreted this structure (which, admittedly, is very difficult to see clearly in the light microscope) as a sort of hood or canopy covering the oral aperture of the ciliate. If you look closely at his illustration, you can see that he has drawn it as a baggy tube.

Calyptotricha's undulating membrane resembles a sail or banner (image adapted from Colin R. Curds, British and Other Freshwater Ciliated Protozoa)

The true shape of Calyptotricha’s undulating membrane (image from Colin R. Curds, British and Other Freshwater Ciliated Protozoa, with arrows added)

Evidently, it was this imagined resemblance to a poke-bonnet that prompted him to give the genus its curious name, Calyptotricha, constructed from the Greek calyptos (“veiled” or “covered”) and trich (“hair”). It seems the “haired” holotrichous ciliate reminded him of a woman’s head, on top which the membrane sits like an old-fashioned hat!

It’s an example of how expectation shapes observation. In interpreting this membrane as an enclosed hood, he was deferring to an earlier error by his illustrious contemporary William Saville Kent. Writing about Pleuronema, Kent says: “[T]his membranous trap may be appropriately compared with the extensile hood of a carriage or an outside windowshade forming, when expanded, a capacious hood-shaped awning, and when not in use being packed away in neat folds close around the animalcule’s mouth.”

The “extensile hood” Kent mentions was a common convenience on carriages of his day, and provided a compelling mechanical analogy for the “neat folds” with which he imagined Pleuronema pulled back its velum.

Barouche image 2Here, for comparison, is Kent’s illustration of Pleuronema chrysalis, which I’ve inverted to showcase its “extensile hood.”

Pleuronema chrysalis, from W. S. Kent's A Manual of Infusoria.  Put wheels on it, and you have a chuck wagon.

With wheels, it would make a good chuck wagon.

To modern workers familiar with the morphology of hymenostome ciliates, as revealed in specimens that have been stained with silver, this is an implausible design. However, to Kent, who had done pioneering work on choanoflagellates, it seemed reasonable to speculate that Pleuronema’s hood might share “a distant homological relationship” with the “delicate funnel-shaped membranes” found in the collared flagellates, which really do wear something a bit like a straw poke-bonnet (but on the back end of the cell).

Finally, since we’ve been talking about Pleuronema and her sisters, I’ll post some footage of one, quietly browsing on bacteria in water taken from a tidal pool on the coast of Maine:

REFERENCES

Dec 092014
 

Eckhard Voelcker (right) with Steffen Clauß

Its been less than half a year since Eckhard Voelcker and Steffen Clauß launched their enchanting online gallery of amoeboid organisms, www.Penard.de. Already, it has emerged as one of the best places to find micrographs of amoebae and heliozoans, and the collection is continuing to grow and improve. The site features some superb light microscopy, but also sumptuously clear and detailed scanning electron micrographs prepared in Eckhards own basement laboratory.

Eckhard is an unusual guy.  A self-taught programmer, he spent several decades in software development (at the head of Völcker Informatik AG) before turning, in midlife, to the exploration of amoeboid protists. He has pursued the new discipline in a remarkably organized and self-assured way, and, in collaboration with Steffen Clauß, has begun to make real contributions to the field. As an amateur scientist working at a high level, Eckhard seemed like a perfect subject for Meet the Protistologist. I contacted him a few weeks ago, and he agreed to answer some questions.

“The child is father of the man,” as the poet Wordsworth said. I would like to know something about your earlier life. Where did you grow up? Were you exposed to the natural sciences as a child?

I grew up in northern Germany. Natural sciences were always my favorite subjects and I wanted to study chemistry or biology. Somehow I ended up becoming a computer scientist and moved to Berlin. Here I started my own software firm a couple of years later. Biology became a hobby of mine and I enjoyed watching microbes with the microscope to relax after work. It was in the year 2010, after a large corporation bought my firm, that I started to think about my future. So I started to plan for an early retirement and went as often as possible to the university, where a friend of mine, Klaus Hausmann, was a professor teaching and researching protistology. After Klaus introduced me to the electron microscope, I was hooked. I planned and built a protistology laboratory with an electron microscope in my basement and decided to focus on this and not software anymore.

So, you had no formal training in protistology or microscopy, before you began to visit Klaus Hausmann’s lab at the Freie Universität Berlin?  Did you do any work at his facility, or were you simply observing?

I had been a member of the Berlin Microscopic Society for some years and my microscopic interest was mainly protists. So I did spend many hours observing, reading papers and studying books. When I would find an amoeba unknown to me, I would try to identify at least the genus and then read the available literature about it. That was why I started with the EM in the first place. I found Cochliopodium amoebae and was interested in the scale structure that is invisible with the light microscope. Somehow I convinced Klaus Hausmann that this would be interesting and he promised to help me learning the EM preparation and operation. There was this magical day a couple of weeks later that I remember so well. I had brought a culture of Cochliopodium vestitum to the university and we put some cover slips in petri dishes and filled these with my culture. A couple of days later it was my birthday and I had decided to take the day off and prepare for the EM. In the afternoon, when the preparation was done, I went to Klaus’s office proudly holding 6 sputter-coated coverslips on EM stubs and together we went down to the SEM. It was a magic moment when I first saw those delicate scales – and it was my first very own preparation (Klaus said I was very lucky to be successful right away – oh boy, was he right). When I had dinner with my wife that evening, I told her, this is what I want to do when I am done with my job. It took me some years though to finalize my work and to build my lab, but now it is all done. Klaus Hausmann has retired two years ago and the lab at the university is not a hotspot for protistology anymore as his successor is focusing on evolution.

Cochliopodium vestitum (source: Eckhard Voelcker).

You’ve mentioned to me that you learn best on your own, outside an academic context. Could you elaborate on that?

It has nothing to do with the academic context. When I listen to a lecture on video, I will pause that lecture a dozen times or so and check something, often to dig deeper into a certain detail. After my curiosity is satisfied, I will continue the lecture. I cannot do this when somebody stands in front of a blackboard “live”.

How did you begin planning your home lab?  You must have been acquiring new knowledge and skills at a prodigious rate.

Planning my lab was fairly easy. I knew what I needed for preparation and there was only one room available anyway. So basically it was just the question, how do you fit a fume hood, refrigerator and deep freezer for chemicals, a SEM, sputter coater and critical point dryer into one room. Originally I planned to leave the light microscopy at my old lab in my study, but this proved to be not practical. So I moved everything down into the lab, although it is a bit cramped now. But as my wife said, this removed the danger of me buying yet another microscope.

Eckhard’s home laboratory, with Zeiss Sigma Scanning Electron Microscope at the left. (Source: Eckhard Voelcker)

Did you have collaborators in the beginning?  Were you already working with Steffen Clauß?

 I got in contact with Ferry Siemensma pretty early. He helped me to identify some amoeba and we have spent many hours on the phone. It was Ferry who brought Steffen and me together. Steffen had found an undescribed testate amoeba and wanted to know how to prepare it for the EM. Eventually we met and got to know each other. We were in the same position, hobbyists working alone with an exotic (to say the least) passion for amoebae. In the spring of this year we came up with the idea to create a website about amoebae combining light- and electron-microscopic images.

So, even at the start you had a particular interest in amoebae. What attracts you to them?

When I had my first small microscope it did not take long to stumble across Arcella discoides. It looked so strange, so perfectly round, simply incredible, like a flying saucer. I realized that there was more to amoebae besides being a blob of slime. The more I looked into amoebae and heliozoans the more fascinated I became.

Have you singled out certain taxa or biological phenomena for closer study? 

I have a special interest in cells with scales. Some of the “naked” amoebae are really not naked, but covered with minute scales of a specific structure. Korotnevella and Cochliopodium are two nice examples. Also some heliozoans, especially Pterocystis fascinate me. When we sample in unspoiled environments, we will find species that have been more or less forgotten since over 100 years and that have never been imaged with an electron microscope. We also find many undescribed species. When I load a preparation into the electron microscope and I see an undescribed species, it really is some kind of golden moment. I am the first human who is seeing this species. But the challenge is to isolate and culture so molecular data can be obtained. Without molecular data you cannot describe new species these days. And publishing what we find is an important goal. I hope that next year we will be able to do this.

Korotnevella sp. looks like a “naked” amoeba in transmitted light, but SEM reveals its cloak of intricate scales. Source: Eckhard Voelcker.

Many of your micrographs are as aesthetically pleasing as they are informative.  Do you have any thoughts about the role of art in science, or science in art?

This is a very interesting question. Most boys of my generation, as some generations before me, received at some point in their youth a microscope as a present. Looking into pond water to see the wonders of paramecium, euglena etc. was very common. Today internet gaming, social media etc. seems to be more popular and „young scientists“, who explore their surrounding nature with the microscope or a looking glass have become very rare. If we want to make people understand, that environmental protection is not only about rare plants and animals, but about unspoiled environments, swamps etc, we need to show them there is something wonderful living in these waters. If we want to make people excited about science, we need to make it visually attractive. I fully understand why most scientists don’t bother about aesthetics in their images. They have little time, are under pressure to produce papers etc. But this will create little public enthusiasm about their work. And this leads to less funding. For Steffen and me, if we can’t show an amoeba in a nice image, we won’t show it at all.

In many natural sciences, even in mathematics, very often the most fundamental equations are very aesthetic.  Look at the mandelbrot set. Or look at some important equations like e = mc2, c2 = a2 + b2, or my favorite one, Euler’s eiπ + 1 = 0 that combines 5 of the most important numbers. And the result is a circle!

Pterocystis, a very small centrohelid surrounded by spathe-like siliceous scales. (Source: Eckhard Voelcker).

The  website you and Steffen Clauß have created to house these images was named for Eugène Penard, and features a touching biography of the great amoebologist. Do you see your research as a revival or continuation of the kind of work he did? Obviously, alpha taxonomy is less ambitious, these days, and proceeds more slowly; but you have tools at your disposal that can open doors that were closed to pioneers like Leidy and Penard…

I think it would be greatly overstating our capabilities and ambitions to call it a revival or continuation of Penard’s work. But we hope that we can fill a niche. We do groundwork, trying to find amoebae hotspots, and scrutinize them for new species etc.

Next year will be a big change. I have retired from my normal job and Steffen will be working in his normal job only 50%, spending the other 50% in protistology with me. This gives us opportunities to become more professional and to isolate species for further investigation and also for sequencing. When you come home from a normal job, your kids demand attention, the cultures demand attention, there are images that need to be processed, species need to be identified … This has been difficult for us and often when we found something that would require more attention and care we would fail due to time restrictions. Our families have been very supportive and understanding but ultimately, there is only so much you can do when you have a normal job and a family. So now that we made all those changes, we have high hopes for the future.

What is the most challenging hurdle to getting into protists, in your opinion?

Getting into protists is easy, the challenge is coming later: finding a job in protistology that is paying!

Given your professional background in computers and software, do you have any thoughts on how IT could provide more support for protist research?

This is something that constantly amazes me. How can a group of such highly intelligent and educated people live with so little IT infrastructure support? Where is our species database? I want to be able to search based on traits. I want to see images. I want to see the latest papers on this subject. I want to know who has seen it, who is interested in it, etc., etc. I think that protist research would greatly benefit from a certain shared infrastructure. If they all would work for the same institution they would have an infrastructure like this in place within in a short period of time. It would make the entire group so much more efficient and the ROI would be quick and high.

Any other thoughts?

Spend less time surfing the internet and more time in front of your microscope. 😉

I will try to follow that advice!  Thanks for taking the time to do this.

Some choanoflagellates (Choanomonada Kent 1880), members of the protist group most closely related to us. (Source: Eckhard Voelcker)

 

Oct 092014
 

As I might have mentioned already, my favorite protists are the shaggy, shapely, fast-moving ciliates. They have a lot to offer the idle protist-ogler. As a group, they include some of the largest and most ridiculous-looking microbes in the pond. Many are easy to identify without expensive equipment or special techniques. Some, like the noodle-necked Lacrymaria olor, can be recognized at a glance in the light microscope, even at low magnification. Others, like the stately Stentors, may need closer inspection for a species-level classification, but can still be identified by prominent features such as the colour of the cell, or the shape and distribution of various organelles.

Unfortunately, not all ciliates are so easy to tell apart.  Some are like the “little brown birds” that plague neophyte birders, and can only be distinguished from one another by very close observation under exacting conditions.  And many, I’m sorry to say, are pretty much impossible to identify, even to genus level, without the help of special stains that expose distinctive patterns in the cilia on the surface of the cell body.

The classic technique for exposing these structures is to fix the cells in some noxious and foul-smelling substance and then soak them in solutions containing various compounds of silver. Certain parts of the organism–most conveniently, for our purposes, the ciliary rows and the nuclei–are “argentophilic,” which is to say they stain darkly when exposed to silver. The ability to selectively stain these organelles revolutionized ciliate taxonomy in the second half of the 20th century, and it is still the most important technique available to modern ciliatology.

Despite my particular interest in ciliates, I’d never tried it until just a few days ago.

I’ve been slow to get around to this, mainly because it’s hard to do. Even the easiest methods of silver staining call for a cupboard full of powders and solvents, none of which is available at Shopper’s Drug Mart, and some of which must be handled and stored very thoughtfully. To procure the ingredients I had to find suppliers willing to do business with an individual buyer, and in some cases I had to pay special transport fees.

lab reagents

Then, of course, I had to assemble the equipment required to use this stuff safely: graduated cylinders, flasks, funnels, fixing jars, an accurate scale, syringes, latex gloves, etc.

lab stuff

And finally, I had to acquire a bunch of new skills.  I haven’t stood at a lab bench since the ninth grade (40 years ago, if you can believe it), so I had to learn how to do simple tasks, like weighing, pouring and mixing.  Fortunately, before undertaking any of this, I had the foresight to culture a full-sized biochemist, which was quite expensive and took about 23 years.  He is currently living in my basement, and was very helpful at several points.

Here, then, is my first attempt at staining a plain old Paramecium by one of the silver carbonate methods:

Silver carbonate Paramecium

Yes, there’s a lot of room for improvement, but, frankly, I’m delighted that it worked at all.

Here’s one more from the same slide, a specimen of a common hymenostome ciliate with the curious name of Glaucoma:

?????????????

The impregnation could be more uniform, the focus could be sharper and the hot spot from the microscope lamp is downright annoying. However, I can count the kineties and easily see the shape of the macronucleus.  That’s a step forward, for me.

The protocol I followed is the one developed by Augustin, Foissner and Adam in 1984 (described in Foissner’s updated guide to basic methods for ciliate taxonomy). I’m told that the original Fernandez-Galiano method gives more consistent results, so I’ll try that next.

 

 

Jun 042014
 
House_centipede

Common House Centipede (Scutigera coleoptrata) Click image for source.

My daughter slept on the couch last night because there was a “giant centipede” in her room. A search on “giant centipede” turns up exotic beauties like the fabulous foot-long Scolopendra gigantea, which eats mice, snakes, lizards, birds and frogs and has even figured out how to catch bats by dangling from cave ceilings .  I doubt that my daughter’s centipede was really a giant–she only needed one hand to show me how big it was.  But it’s another reminder, if we need one, that “nature” is not off in the woods somewhere, and you don’t have to paddle to it, or ride there on an ATV.  It is under the floorboards and between the threads of our sheets.  It’s us, and it’s all over us.  As science writers like to remind us, our own skins are a fertile savannah to the microbes and mites that browse in its moist valleys and fungal thickets.  Our intestines are as lush and biologically diverse as a jungle, an Amazon you can carry around.

Too often, though, we think of nature as something that had better not be scrabbling up the leg of the bed.  It belongs in certain places, and we do like to put things where they belong.  The urge to sort things, to put them in their place, is strong in us and features prominently in lists of human universals.  When things are in the “wrong” place, we tend to not see them properly, or to not see them at all.  Take the contents of any contemporary art museum and put them out by the side of the road.  I’m pretty sure some of the artwork will still be there the next day; and some of it will probably sit there long enough to be hauled away with the trash on Wednesday morning.  Leaving aside the likelihood that the landfill is the right place for some of it, this is a small failure of perception, one that is so common and familiar that we design our public spaces to allow for it.  We have trouble seeing the art, even when it is in front of our eyes.  So, we label the art, or lift it off the ground on a slab of stone, or we build places like museums and galleries where the right kind of seeing and thinking is gently encouraged.

Seeing “nature” is almost as hard as seeing “art”. To make it possible to notice nature, we set some of it aside in special spots.  These are our sanctuaries and conservation zones: places where we can look at what would be here if we were not.  We choose a patch of ground, or pool of water–often, I’m sorry to say, one that nobody wants for anything else–and we do with it something that does not come naturally to us, something that is not “in our nature”: we leave it alone.  We just leave it to itself, so that we can go there once in a while, and look at it to see what things are like when we are not around.  Except that we are around, of course, stealthily watching.  We are there and not there at the same time.  This gives us a feeling we find so agreeable that we are willing to tax one other to pay for it all: the boardwalks and the picnic tables, the bilingual signs warning us not to interfere with it in any way.

A marsh in the Mer Bleue Conservation Area

A marsh in the Mer Bleue Conservation Area

For a couple of years, I’ve been going to one of those places as often as I can.  It is the Mer Bleue Bog, a patch of subarctic peatland inside Ottawa’s city limits.  At one time, the Ottawa River ran directly through it, but then the course of the river changed, leaving it hydrologically isolated, fed only by rainwater. For about 8,400 years, sphagnum moss has been accumulating there, to a depth of 6 metres in some places.  It is an unbroken link to the end of the last ice age, and although the city and its commercial sprawl are not far away, it has an eerie–I was about to say “unnatural”–calm that seems to startle its many visitors into speaking very quietly, as if they were in a church.

There is still some open water attached to the bog, including a cattail marsh where I collect samples to look at under the microscope.  It is what lake researchers–“limnologists”–call a “dystrophic lake.” The water is low in nutrients, highly acidic and steeped in humus.  It is the colour of a weak tea, one that happens to be filled with the most wonderful algae, ciliates and amoebae.

The chemistry of the water, and the isolation of the entire system, give it a distinctive microlife, quite different from anything in the other lakes and rivers around here.  It is much greener, for one thing.  Perhaps because it is so poor in available nutrients, many of the organisms here make their own food by photosynthesis.  In this water, I’ve found a surprising diversity of protists, including many that don’t turn up in my usual samples,and a few that have never been described before.

A new testate amoeba in the genus Arcella.

A new testate amoeba in the genus Arcella.

Some are different enough to deserve new names of their own. The most recent novelty to turn up in my jars is a testate amoeba of the genus Arcella, a creature that lives in a rather pretty proteinaceous shell.  This one resembles an amoeba described in 1918 by Playfair, Arcella costata var. angulosa.  However, it is distinct enough from anything previously described that, in the opinion of Arcella expert Ralf Meisterfeld (in personal communication), it is “certainly a new species.”

 

 

Arcella ventral view 1

Ventral view showing crenulated pseudostome.

The  main feature that sets it apart is the shape of the aperture at the bottom of the shell.  This “pseudostome” (“false mouth”) is an opening in the shell through which the amoeba extends its pseudopods.  In most Arcella it is smooth and round, but in these guys it has a frilly, “crenulated” shape, like a malformed flower. I wonder if this is a strictly local variation, or something that is found elsewhere in the world?  I would like to think it arose locally in the Mer Bleue population, perhaps because of its isolation from the surrounding waters; however, it is likely that the feature is found in many other populations, but has rarely been recorded. This line of thought risks reanimating the perpetual debate about whether microbial species have a discernible biogeography, as lemurs and wombats do. I’ll leave that alone for now, but it deserves a post of its own.

In the meantime, here’s some video of  this little jewel:

 

 

Mar 262014
 
Paddy 2

David “Paddy” Patterson

David J. Patterson–known to friends and colleagues as “Paddy”–is a major figure in eukaryote taxonomy, evolutionary protistology and biodiversity informatics. In the 42 years since his first paper was published (a nifty little study of habituation in Vorticella) he has done enough work for several ordinary careers. With various collaborators, he has added some 250 new taxa to the eukaryote family tree (stramenopiles, Cristamonadida, ramicristates, Centramoebida, among many more), and has had a hand in the early description of a remarkable number of organisms, such as Cafeteria, Carpediemonas, many flavours of Nuclearia and such intriguingly-named creatures as Kamera lens, Macapella, and Massisteria. Anyone doing research on Centrohelida, Nucleariida or heterotrophic flagellates of any kind will find themselves, at some point, following his tracks in the snow.

In the past decade, he has been at the forefront of the effort to put biological diversity online, nudging protistology into the “Big Data World.” An early project in this field was his online database of microbial life, micro*scope, and its sister site bio*pedia. Though the software now rattles and clanks like an old tractor, micro*scope still provides a home for some of the best collections of high-quality, peer-reviewed images of protists on the internet. While preparing this interview, I was delighted to discover that it is once again online and fully interactive at a new address.

I interrogated Paddy by Skype, in late November of 2013, but it was several months before I got up the nerve to pass his very fluent and erudite answers through the microtome. Our conversation ran largely to taxonomy and bioinformatics, and the miseries of microbe identification, which left little time to discuss his four decades in protistology. I hope to remedy that, at some point in the future. In the meantime, here is a fairly thin slice of Paddy.

First, where are you now?

You’re speaking to me in Arizona, at the moment. I’m originally Irish, worked in England for 17 years, and then went to University of Sydney where I became head of Biological Sciences. I have a house there, so that’s where I think is home. For most of the last nine years I’ve been working in the U.S.

In 2004, you went to the Woods Hole Marine Biological Laboratory.

 At that time I had an idea that you could use taxonomy as a device in the emerging internet to start joining together information about organisms better than the standard search engines could do, because if you’re playing with taxonomy you understand issues like hierarchies, and the value of hierarchies, and you understand that there are different spellings for organism names and that there are many different names for organisms, different opinions leading to synonymies, vernacular names and so on. Taxonomists are the guys who know all about that stuff, know how to manage it. The idea was to build a digital infrastructure that calls on name so that it can organize all biological information on any species. That was the idea that was the nucleus of the Encyclopedia of Life. I led the informatics team that established the EOL.

You’ve moved on to other things, since then?

Well, I am still in the same vein. Somewhere round about 2000, mostly because of the inaccurate delivery estimates of a shipping company (called Australian Van Lines, not to name anyone in particular), I was unable to write a book that I’d intended to write and my intentions turned more to moving information onto the internet because it was very clear that that would be where people would seek information. Now the process is almost 100 percent complete. It was that need to think of ways to integrate distributed information, because biological data, in our case, is emerging on more than tens of thousands of websites. Each carries fragments of information, some overlapping, some independent. I began to explore how to join the information together and enable the community to contribute, with the micro*scope website. The result was a communal environment that relied on a names-based infrastructure. EOL was the realization of the same idea for all organisms. However, the ideas, tools and services were not available to others, and what has been driving me since then is to promote the development of an infrastructure that is independent of any project. Then we can all use it to combine and filter the distributed data; there is an incentive to collaborate, and to share individual progress. That’s what’s been keeping me busy since EOL.

You’ve been something of a champion of name-based taxonomy, over some of the other options (barcoding, for instance).

I wouldn’t say that. The best approach has to be considered a bit more carefully, because it depends on what the objectives are. Everything that emerges in the world of science has value, and we should never ever dismiss any element.

Massisteria

The cercomonad flagellate Massisteria. Image by D. J. Patterson, from micro*scope (click for source)

One of my biggest concerns about science, just thinking about the way it’s grown over the last 200 years or so, has been its faddishness, its tendency to have fashions and for new technologies to knock out older approaches. The shift, coupled with competition for research funding, quickly leads to the argument that older approaches have no longer got any value. The consequence is to go forward with a new technology and dismiss the old ones. Certainly, in the area of alpha taxonomy, observational taxonomy–the kind of thing that you enjoy doing and that I’ve spent a lot of time at–still has an immeasurable amount of value to give in lots of different ways. The observational approach will continue to be a source for discovery. Our observations on diversity are enriched with environmental information, information on the composition of the community, its dynamics, and the various ecological transactions that take place in nature. There is an enlivening value that comes out of watching organisms of all kinds, but especially with microorganisms because you can provide students with an opportunity to get access to many species in a short period of time, in such a small place. Most of us who watch microbes enjoy that experience enormously, and we can watch school kids and students in universities becoming inspired about biology, about the microbial world, about nature through that. So I rate the observational side of things very highly and, yes, I am fearful that the new technologies like the molecular barcoding will simply knock out the old stuff, leaving us with problems, as insights are disconnected from all the old stuff, and we have an impoverished view of Nature.

Clearly, this is not an either/or situation; although competition for funds lead many to project it as if it were. Rather, we have to build bridges. If we don’t invest in finding the technology to create such bridges, then the old stuff is likely to get forgotten, and a new molecular description will take over.  If that is not managed, we will have to redescribe all that we know through molecular techniques; and there are invaluable and irreplaceable historical observations that will be lost. The informatics tools and services are emerging, and that will link information together–as long as it is digital and openly accessible [on] the internet. One useful and immediate task is for those who explore diversity through molecular tools to keep voucher specimens, so that they are able to say, “This sequence came from this particular specimen, or this species. I don’t know what the species is, but this is the thing I’ve got the sequence of information from.” And if they can put that onto the internet somewhere, then you and I may be able to say, “Hey, I know what that species is.” Then by just adding the name, the infrastructure will be able to connect the new molecular observations to all of the information about that species that’s available from the time Leeuwenhoek forward.

Looking back over the 300 years since Leeuwenhoek, the effort that’s gone into classification is staggering. The loss of all that work would make a person sad, even if it were not still useful, scientifically.

There is a bit of that that I absolutely agree with. Looking at the way folk tried to sort out all this diversity over a period or 200-250 years helps us a lot to understand fashions in science and the ways things can go wrong. If you’re attuned to the history you can then watch the present and say, “We’re remaking a mistake of this kind.” We should also be able to look at history and not just think about the way that people do things, but start assembling a suite of principles that can guide best practices. One of my biggest concerns about systematic protistology is the failure of good principled approaches to dominate over crappy approaches. And there’s a lot of crap in systematic protistology. A lot. I mean, it’s bad, in my view, terribly bad.

Researching an organism, I often find myself on a moebius strip of identification, because of the insufficient descriptions that are out there…the competing descriptions of the same organisms.

Again, you could build the answer to this.  The solution doesn’t exist as a single item. The perspectives you talk about are different points of view. Different folk look at the problem from their own perspective and from their own biases, and so you get many different variations on the theme. Each one usually has something special to add. But also, no document is complete. But, novices especially can’t see the signal for the noise. If you’re in this kind of unclear zone, it is easy to get lost and confused.

The answer to me is simple, and we ought to do it straight away, and it only needs a little bit of money.  (Well, probably a fair bit of money!). It relies on accumulating knowledge in little bits, empowering everyone to be part of the process, and having a mechanism by which anyone interested can criticise and evaluate content. The Wikipedia model is great. Begin with a communal classification structure in which the hierarchical component is independent of the terminal taxa, so that you can have multiple classifications of the same species arranged in different ways. That would then allow a user to have a classification like, say, the Adl et al. classification, if that’s what we want, or the Margulis classification, if that’s what you want, or a Cavalier-Smith classification, if that’s what you want, or one that is principled and defensible if that is what you want.

The separation of organizing the classification from the terminal entities gives you flexibility for new insights or different points of view. Once we have a communal catalogue of terminal taxa that allows you to remove all those false Didinium species [Editorial Note: Paddy is referring to six non-existent Didinium species that have spread by “database contagion” to many  sites on the internet], we can begin the process of annotating most of those taxa with descriptive information, ideally as what they might call semantically minimal units. Things that would just say: Minimum length? Give a number. Maximum length? Give a number. Minimum width? Give a number. Maximum width? Give a number. Just think of all the descriptive features and find a way to break it down so that you have one-word answers to input.  This approach can be accelerated by using defensible hierarchies to annotate all children with the same information (one data entry should annotate all ciliate species with the statement: “Primitively with macronucleus and micronucleus”).

Paddy 1Another advantage of annotating taxa with atoms of information is that the resulting matrix can be used in a filtering approach to identification. I think we talked about it once using the example of Lucid keys. What Lucid does is to create a grid that includes all the species that the maker knows about and here are all the attributes. To identify the taxon, you simply say, “It’s from freshwater,” and immediately everything that is not known to ever occur in fresh water is eliminated from your system.  You can then say, “…and it’s 23 microns long,” and everything that doesn’t have 23 in between minimum and maximum is thrown out as well; and you say, “It’s got 2 flagella and everything that doesn’t have 2 flagella is thrown out. You shorten the list extremely quickly. At some point you can say, “Ach, I can’t go any further, I’ve got no more characters, but we’ve only got seven species left on the list, show me pictures of them.” That would take you to a gallery of those seven species: which one do you think you’ve got?

And building that is elementary, it’s not a challenge in any way to build such a structure. The challenge is to populate it with data.  That would take a lot of time. But that’s the kind of thing which a community of protistologists can easily do as a communal on-line endeavour. The current research paradigm, in my view, is never going to build that structure because it’s going to take too long, because it requires resources distributed to a large community of experts, and that’s not the way research works. But a society, or group of enthusiasts could say, “Well, why don’t we make this system and make it as an open and communally available system,” [and] then it could happen.

And something like the micro*scope environment could be adapted to that kind of thing. You already have a classification in there, there’s a place where it can be edited. Micro*scope is the kind of environment that could be used to create such a structure.

For identification purposes, micro*scope is still the most useful site on the web, by a long stretch.

It’s in its death throes, to be honest. Unless somebody very generous comes up with a heap of money that would allow some, what they call, refactoring of the software, it’s not going to survive much longer. Which is a shame. But that reveals a problem with infrastructure: it needs sustained funding.  The answer for that probably lies with support from societies or institutions.

Much of the other stuff on the web has not been competently reviewed. There’s a sort of echo effect…when bad information gets out there it reinforces itself.

And it’s often repeated as well, but yes, you’re right. You know I was hunting for something the other day, and what was coming up under image search was just amazing, just so badly identified. There’s a carelessness with so many people, about protistan identification, even by specialists. It’s very worrisome. I have a fairly negative view about the standards that protistologists set themselves; I think they generally set very, very loose standards.

What about the future of morphological identification, in general?  In some groups it’s become increasingly difficult to identify organisms, at least with the light microscope.

Yes, there’s always been problems about how much information you can get from a light microscope, and whether it’s appropriate to what you think is the diversity inside any group. If identification is the only thing you’re concerned about, in my view we should just absolutely and enthusiastically embrace various molecular technologies. We should start off by a major effort to get reference material for each taxon sequenced so that we can match new or environmental samples against this reference structure. If, after that, all you want to know is who’s living in a particular place, the best thing to do in the future would be just to put out a sample and mash it up and analyze the total DNA for all the sequences in there.

The trouble is, most don’t want to know a list of names of things that are in that pond.  They actually want to see the organisms, they want to watch them. They want to identify after they’ve observed them…and they won’t have access to molecular tools, so you’re back to that world in which microscopes are needed. Again, as before, either/or is not the way to approach this. We need both, and that means, for the molecular community, they need to assemble [quite a large amount of] reference material.  And I don’t think it’s that hard to do. It’s just getting a heap of people enthused to work together to populate the environment we will need.

Maybe it would help to enlist amateurs like me, in an organized way, to fill in some of those gaps?

You can take charge of it!  And there are, around the world, some very good amateur observers–often more interested in microalgae than protozoa–but they are out there. Societies could endorse their efforts as well, and societies could be looking at training exercises for kids in schools, for example, but that can also add to the infrastructure that we all might use.

Looking from the outside at biodiversity informatics, it seems to me there are a lot of competing projects. How much overlap is there between all the different databases out there?

Before we might talk about some particulars, one thing that we haven’t been doing is to distinguish the conduct of research from the assembly of infrastructure. Bioinformatics is as much an issue of infrastructure as research. Research is typically done with short-term projects that last 3-5 years. Typically, there’s an uncertainty about whether the research will ever be done. People write proposals, and they may or may not get funded, so there’s a kind of uncertainty in there. Typically, in an area, you’re going to have an array of individuals and small groups conducting research.

So, let’s say, in ciliate diversity you’ve got the Foissner group, you’ve got Weibo Song’s group, Denis Lynn…a lot of people. You don’t ever think about those guys as overlapping, of there being any redundancy in there. We don’t want to have a situation where there’s only one person, because then you will have a single point of failure, and you lose the diversity of people and their approaches, something we value in research.

Infrastructure is not the same. During the early phases of development of an infrastructure, it really is very, very good to have diversity.  This redundancy should not be condemned, it should be welcomed.  That said, I agree there is too much wheel rebuilding within biodiversity informatics infrastructure.  The reason is that there is simply no paradigm for funding infrastructure. There’s no mechanism by which we can say, well, what we want to do is to build an infrastructure and it’s got to live in perpetuity, at least as far as we can imagine. It’s going to serve lots of people. Once you have worked out a suitable approach, we need only one infrastructure, but one that’s going to serve lots of research teams all around the world. To do this, we would like to have money for at least the next 10 years — at least. There’s no mechanism to achieve that, currently. So we end up having the situation where everybody argues that they’re building infrastructure but have to present it as innovative research. The result are many competing systems justified [as] being better than the others out there.  And then you get duplication. So, the solution is in establishing a different kind of funding paradigm for infrastructure.

pseudovorticella pattersoni

Pseudovorticella pattersoni, one of many species named for Paddy. From micro*scope (click image for source)

In my view, funding agencies have to acknowledge the need for infrastructure for this big data world, to set aside special funds for special funding conditions to allow the infrastructure to be built, with the expectation that the infrastructure is going to be promoted by large consortia of players, ideally all the players in the game, with the peak of funding at the beginning, to get the system in place, but then long-term funding to ensure that it stays there for the long haul.

Ideally, what we would like is, if you publish a paper about a new species of Paramecium (of which there are many, by the way) immediately, the infrastructure gets populated with this information. You would like to see it in a definitive online classification. It should just happen like that! Done. The technology is there, it’s already in place. If you publish a species in the Pensoft series of journals, their workflow captures that information–that’s a new species!–before the paper ever comes out, sends the information over to Zoobank, and the information’s sitting waiting on Zoobank, so the moment that the paper is actually published, a switch is flipped and the information shows in Zoobank. There’s no reason why all journals cannot have this kind of instant publishing system. Once in that digital space, the new information can flow to other environments, such as EOL.

What projects like Catalogue of Life do is to rely on some decrepit expert person. I mean, every taxonomist has a limit to how many taxa they know.  Usually it’s around a thousand. Anyone who really knows more than a thousand taxa is remarkable, and even a thousand is doing pretty well, for many.  And yet you get these global species databases being created by some individual and they have many, many more than 1000 taxa in them, so it cannot be definitive, they’re going to be wrong. That person is kind of borrowing stuff, guessing what the right status is for these taxa, so you get a sloppy system, you get a system that’s out of date.  It doesn’t maintain currency.  And the other bit that’s absolutely missing is a mechanism for users to enter in criticisms, or comments or improvements, or corrections.  The technology for that also exists, it’s just not being adopted by any of these players.  I mean, clearly, what you’d really like is when you go to something like Catalogue of Life and you say what species are there in the genus Paramecium and it comes up with this little list of 6 or 7 species and I know that there are at least 28 good species in Paramecium, I would like to say, well, what about…and then run the list of them, or feed them in, but their architecture, their workflow, just doesn’t permit that.  And that way it stays bad, and so…

[interrupting] Your vision for EOL was that it would incorporate that sort of feedback from users…

Yes, and they achieved a system a bit like that, but not exactly the way I wanted.  Certainly, when I was thinking about that it wasn’t in the normal style of the contemporary systems.

So, the ideal thing to minimize duplication is that you identify uniquely every piece of information that’s made available…doesn’t matter where it is or what it is.  So, if you have a number that’s long enough you can make an index number that’s going to cover everything that’s ever going to happen in the world.  These big (32 digit) numbers are called “universal unique identifiers” (UUIDs), so every statement everywhere, every piece of information can have one of these things attached to it.

carpediemonad_atw

Carpediemonas sp. Image by D. J. Patterson, from micro*scope (click for source)

The solution to data quality improvement in my view is annotation, which is a technology that’s been around for some time.  It’s well in place in some areas, but not in biology.  And what annotation does is it monitors things with those UUIDs, and then provides a little kind of plug-in to your computer, so if you’re reading something with your browser every single item, such as a name in COL, is distinguished with its own UUID. If we see something such as a misspelling you can click on it, using your little plugin, and out will come a commentary panel, probably a drop-down menu, and you say, “Misspelling?” and you submit. Now, that comment, that annotation, is attached to that UUID, which is attached to a piece of data. That should flow back to where that piece of information first came from, so Catalogue of Life should suddenly get a message popup saying, “Ah, Brucie over there, he’s just decided that there’s an error in this. You should check this out.” It also means that anybody else who looks at the same data should also be able to have a panel where they can see any comments.  So they’d know that there may be doubts about this. But in principle, you could start putting annotations against all of those misidentifications, or soft identifications, saying “I’m not sure these guys have identified this thing right.  It doesn’t gel with the thing I’ve seen over in that website.” The technology to build that kind of system is there.

Are there enough young taxonomists being produced by the universities. Are they being turned out in sufficient number to handle the load?

You shouldn’t have asked the “handle the load” bit of the question, you should have just stopped with the first bit, because that takes you into the area of what “load” is. I think the answer is “No, there is not.” You can understand the problem with universities, that they must justify themselves by preparing students for the work force, and the students need to feel confident that they’ve got an array of skills that are going to position them to be competitive within the work force. And so, if we train them in out-of-date areas that the workplace doesn’t require, like looking at protozoa down a microscope, then we’re not serving the students well, and if we’re not serving the students well the universities are not going to get applause, and they’re going to go backwards.

So, there’s a lot of pressure to keep moving forwards in using all the new technologies.  But I honestly cannot see how you can say you have properly trained a biologist if you don’t build skills in looking at organisms, because it’s only through knowing the organisms and watching them that you know what questions to start asking. And if you don’t have that bit of the game, then somehow you’ve become a charlatan. You’re picking up someone else’s questions and using them. You’ve become just a workman, no longer a visionary.

But then you said “load,” and the question becomes what might “load” be? And I don’t know how I would answer that. I think these days the general sense is that the load that taxonomists have to carry is getting smaller because people don’t seem to want taxonomists very much, so how much load do they have to carry?

Why? What has changed?

I think the promise of the molecular technologies has led to serious questions as to whether traditional taxonomy is an appropriate way of recording biodiversity.

Somebody used the word “quaint” in an article I was reading, suggesting that there was something outmoded about it.

Yes, there’s a lot in that. I think a lot of the alpha taxonomists can be fairly irresponsible in terms of how much energy and time they’re willing to invest in a very small problem. But that also takes you into the fact that taxonomy is actually very expensive to do. Very expensive. Because good taxonomy relies on people with a lot of experience, so you’re going up in the salary level and you need to invest a lot of time. I mean, you imagine how much time it takes to get a good identification of a single species, especially if it’s in one of the nasty genera.

Never mind revise an entire group...

Or provide a catalogue for what’s in a pond.

You have done a lot of popular outreach, with books aimed at a general readership, like Free-living Freshwater Protozoa, and Seen and Unseen: Discovering the microbes of Yellowstone. What prompted you to write for the public?

Well, it came out of being a university teacher.  It’s just part that environment.  What was very obvious to me as a teacher was that in trying to teach people about protozoa, or a protozoan perspective on things.  There are many topics that are greatly enriched by taking a microbial or protistan perspective, cell biology being an outstanding example, because if you want to find what cells have got and what they can do with it, you go look at protist cells, you don’t get as good insights by looking at mammal cells or anything like that.  Ecology, trying to understand ecosystems and the general rules of ecosystems: most of them break when you go down to the tiny guys, because there are so many different factors at play, and you don’t have a reasonable and fair grasp of ecology unless you can cover the full spectrum.

But yet, trying to teach people these things in university, I found I was at a massive disadvantage over those who were teaching about, say, flowering plants or birds, because everybody knows what a bird looks like and they know how they behave and they know much of their biology just from common knowledge; ditto plants, ditto larger organisms.  And yet when you start trying to tell people about protists, they have no idea what kind of organisms you’re talking about, no idea of where they live, how they live, what all the terms are, so you have to go back a lot earlier in the educational process. Plus, I was watching others dealing with the same problem that you were talking about at the beginning, which is, bad identification. Both of those issues can be addressed by trying to introduce a microbial perspective, or a protistan perspective, into peoples’ awareness at a much earlier stage than we currently do. And there were things like the color atlas book, there was another book that was for prawn farms, oddly enough–because they’re kind of interesting environments, microbially speaking–sewage farms are always very interesting.

So, from the books then came micro*scope, which again has the same kind of purpose, but that one, the thing that was driving me for that was partly to get knowledge onto the internet because I came to the conclusion that in the future–this was in 1999, 2000–people were not going to go to books for their information, they were going to go to the internet. So, the intent was to get as much as possible into websites.  But a second big driver for micro*scope was actually the poor quality of the micrographs that were then available on the internet.

In those days, the micrographs were just absolutely terrible.  Well, you’d have the misidentification, you’d have bright fields, you wouldn’t have any contrast, you’d have no reference to the defining features of the organisms. You wouldn’t see the things you really needed to see, to know that it was what it was. You’d have dust and other junk over it, you’d get two thirds of the organisms, because it moved when the photograph was being taken, and its tail’s off the end of the picture. Or they were fixed, which was not at all helpful if you were working with living material. So, one of the drivers behind micro*scope was to make the sure that the site was made a rich and rewarding place to go into and look around, because the pictures were strong visually.

Where did you get the name Paddy?

In Northern Ireland, adding a “Y” onto somebody’s name is the normal way of creating a diminutive, so William is usually Billy, James is Jamesy, Jim is Jimmy, and with a name like Patterson it was the Patterson bit that got the diminutive, so it was shortened to Paddy.  My sister my brother and I were all called Paddy, so when somebody would ring the house and ask for Paddy they’d have to work out which one they were talking about. I’m the only one who hung onto it; but I hung onto it because Paddy is also the word English people use for Irishmen, and to call someone a Paddy is to declare them to be stupid and definitely a lesser form of life than a human being, let alone an English human being: a very derogatory stance that the English take to Irish generally (or to the rest of the world, generally, in fact.  So, my first day at University of Bristol after being appointed to be a lecturer, I was going around to introduce myself to various people. I came up to one room and the door was open, and there were two guys talking in there, and one of them said, “I hear we’ve just appointed a Paddy as a new lecturer.” And so I knocked on the door and I walked in and said “Hi, I’m Paddy.” Since then it’s stuck, professionally as well as privately.

I want to ask about a genus that was named after you.

Pattersoniella vitiphila?

Pattersoniella vitiphila by Foissner

Pattersoniella vitiphila (drawing by Wilhelm Foissner, from Helmut Berger’s Monograph of the Oxytrichidae, 1999) Click Image for link to the book.

Yes, in one of the descriptions on EOL it’s described as “A real cutey, from Fiji.”

Vitiphila is the wrong name, it should actually be “vitiensis.”   “Vitiensis” would mean, “…of Fiji.” So, way, way back I heard that the Royal Society of London had been donated money in the 19th and early 20th centuries to help scientists to carry out field work.  By the time we got to the 1970s and 80s, nobody really did much field work and the money wasn’t being used.  So I wrote to the Royal Society and said, do you know, I have this thing that I think is important to work on, and that is to work out whether protozoa have biogeography. And the way I think we should do that is to compare a list of species that one finds one place that has been well studied, such as Bristol, which is where I was, with somewhere that has hardly been studied at all, and if we find the same species in both places then we’ve got cosmopolitanism and if we have that are very different then we’ve got endemism, and the place that I recommend you send me to, with my microscope, is Fiji. And they said “Yes.” So they sent me to Fiji, and then that began a whole series of studies on biogeography. That ciliate was found during that trip to Fiji, sent to Willi [Foissner] and I asked him to use the name “vitiphila” which is “likes Fiji” rather than “of Fiji.”

As long as we’re talking about protist biogeography, where do you stand on that?

The answer will depend on the level of resolution that you wish to apply.  Obviously, at any level everything has got an endemism. I mean, you are an entity and you have very limited distribution. I am an entity and I have a distribution that barely overlaps with yours; but Homo sapiens is a different entity: cruder resolution, worldwide distribution. At the level of biodiversity that interests me, which is morphological distinctiveness, the vast majority of protists are cosmopolitan. There are going to be a few that are not, but we found things like Postgaardi, which is a flagellate, down near the bottom of euglenozoan territory, which lives in very, very strange anoxic, hypersaline environments, and it was originally found somewhere up in the Arctic circle; and the next time it’s found it’s somewhere in Australia; then it’s found somewhere in the Antarctic. When you’ve only got the one record you’re thinking, well, this could be endemic, and as time goes by, more observations are made, and you pick it up elsewhere. Endemism changes to cosmopolitanism.

Cafeteria roenbergensis

The weed species Cafeteria roenbergensis. Image by D. J. Patterson, from micro*scope.

I mean, people would send me bottles of water, at one stage, when I would doing this microbial biodiversity stuff for marine ecosystems…they would say, “We’ve just been taking water samples, and there’s a flagellate in here that’s in vast numbers, and it’s obviously got big, important influence on the ecosystem, and we’d like somebody to identify it, and we don’t know how to identify it, so we’re sending it to you, could you identify it, because you’re a specialist.”  And I would say, yes, it’s Cafeteria roenbergensis, and I would tell them that without opening the bottle, and I was almost invariably right. Because it’s the most common thing, and when you collect something and you grow it for a while, the weeds dominate and knock everything else out, and Cafeteria‘s one of them.

You should be asking me questions about names like “Cafeteria“…and “Massisteria.”

And “Carpediemonas“…

That was named after my wife who was another protistologist, but she died in ’94. That was after her, because her motto, in life, was “carpe diem.” Carpediemonas was one of the ones she had worked on.  And then Alastair [Simpson] came up with Ergobibamus, “So, let us drink.”  And we wanted to create another one for Gaudeamus, “and be happy,” but Gaudeamus has been picked up by somebody else for some kind of fossil mole, or some piece of junk like that. I enjoy names that are sonorous and amusing.

What is some of the work you’re most happy to have done?

Stephanopogon

Diagram of Stephanopogon cortical ultrastructure in the mouth region, by D. J. Patterson. Click image for Source.

There was an approach to evolutionary systematics that I really valued that came up as a kind of variant form of cladistics and that was called transformed cladistics, and it gave greatest emphasis to the evolutionary novelties that defined new branches in the tree of life. And I held then, when I started learning about that in the eighties–and still do–that it was almost certainly the most sensible way forward. And there was a heap of papers where I started to explore issues like that and to criticize other approaches to evolutionary analyses. There’s a paper on Opalina, that I did, in which is a little tree and it looks very, very simple at the back but it’s one of these ones that…here’s the tree and here are the events that define each of the lines of the tree. That to me was the way things ought to be done, I still think it’s the way it ought to be done.  I came up with some new group names, including Slopalinida — which is one of the names I wish I hadn’t come up with–but it was sensu lato Opalinida, so it took the Opalinida and expanded it.   The stramenopiles paper is always something that I think was a very good one. There’s a paper with a guy called Robin Smith, where we compared different ways of analyzing data on heliozoa. We showed that A) no algorithm gave a better result than any other one, and B) what emerges from all of the analysis as a kind of consensus we knew anyway so a lot of subsequent analysis is just a waste of time. It’s always nice to say that, yeah, you’re all wasting your time!  The Stephanopogon paper is one that I like a lot. I liked the paper, and I liked doing the drawing of the mouth.

Do you enjoy drawing?

I used to, until the day I sat down, put my pen to the paper and couldn’t see the tip of the pen. That was annoying. That was the day my eyes decided they’d got too old to work properly.

 

 

 

 

 

 

Dec 182013
 

Early last year, the mayor of Salzburg proudly announced the creation of a new conservation zone around this “globally unique ‘natural monument'”:

Krauthugel

Click image for source,

The newly protected feature is not that rocky bluff, Festungsberg hill, or the 11th-century fortress that sits on top of it. It is the long, narrow puddle in the foreground.  This is Krauthügel Pond, an ephemeral body of water barely 30 cm deep where researchers have found 121 species of ciliates, ten of them previously undescribed. Because of these organisms–five of which have not been found elsewhere–Salzburg now possesses the world’s first second “Natural Monument for Single-celled Organisms.” A protist wildlife sanctuary!

The pond comes and goes during the year, appearing after heavy rains on a raised agricultural plot known as Krauthügel, or “cabbage hill.” The bed in which it lies is thought to be the remains of an old stream, whose natural course might have been altered by agriculture during the middle ages. Since then, roadwork and urban development have isolated the body from other surrounding channels.

From 1789 until 1960, the field was used for raising vegetables.  After that, it became a pasture. For about thirty years, cows trampled the soft turf and nourished the local microbes with their  manure, creating what ecologists call a “eutrophied pond.” In other words, a cattle wallow, or slough.

This is not what you could call a pristine natural environment. It doesn’t shelter any large, charismatic animals. It is not particularly scenic, when it can be seen at all (much of the year, the “pond” is dry). In short: it’s hard to imagine a patch of ground less likely to be singled out for conservation.

However, Krauthügel Pond has something your local ditches and mudholes lack: proximity to Wilhelm Foissner, an astonishingly productive ciliatologist who happens to live and work in Salzburg.

Foissner

Wilhelm Foissner (Click Image for Source)

Arguably, the “natural wonder” here is not so much Krauthügel pond as Professor Foissner, whose vast body of work looms over modern ciliate systematics like the Festungsberg itself. With five or six hundred publications to his name–at least three hundred in peer-reviewed journals–Foissner, working alone or in collaboration, has discovered and described over 500 new protist species.  If there were new ciliates in your cow field, he would be the man to find them.

Actually, to see a new species is not that unusual.  Likely, we all run across undescribed organisms, from time to time, without knowing it. The little red bug that alights on your arm might be something never before recorded in the literature, if only you knew. Place samples of local mud under the microscope, and you are quite likely to find organisms that don’t yet have names. Of course, it’s one thing to see something new as it paddles by, and quite another to know what you have seen. To properly document your discovery, and publish the news of it, requires skills and technology that are in extremely short supply.

So, these ciliates were pretty lucky to have been born in Salzburg, near one of the few people in the world with the ability (and inclination) to see them for what they are and lobby for their protection. It raises some interesting questions.

First, how exceptional is the microbe diversity that has been preserved in Krauthügel?  In a report on the the pond, published earlier this year, Fenton P.D. Cotterill and his co-authors compare the ciliate species count at their location to various “well-investigated ephemeral waters” in other parts of the world: two meltwater ponds in Southwestern Ontario, a roadside puddle in Namibia, a rock pool in Venezuela, a meadow in Hungary, and several other choice spots.  They find that the Salzburg pond is in the “upper range” for total number of species, but only in the “middle range” for the number of new species.

Evidently, the old cabbage field supports a high–but far from unique–diversity, and when closely probed by the best protistologists in the business, it yields about the expected number of new organisms. A rich but fairly ordinary body of water, it seems.  Why single it out for protection?

Three species only found at Krauthügel  e)  Semispathidium pulchrum f) Papillorhabdos multinucleatus g) Fuscheria nodosa salisburgensis

Three species only found at Krauthügel e) Semispathidium pulchrum f) Papillorhabdos multinucleatus g) Fuscheria nodosa salisburgensis

There are a couple of reasons. First, as the authors point out, appeals for conservation are usually based “on the narrow distribution of one or several species and their habitat, or of species and habitats endangered by human activities.”  If a forest supports the only known population of Sibree’s Dwarf Lemur, we have reason to preserve it, because if we don’t, we can expect to lose that species forever. By that standard–provided we suppress the size-bias that can make us indifferent to the fate of a microbial species–the case for protecting Krauthügel is pretty strong.  As of April, 2013, five of the the ten new species found there had “not been reported from any other locality.”  Until they turn up elsewhere, those five species are assumed to be “endemic” to Salzburg (that is, restricted to that area).  Given the scarcity of competent ciliatologists in other parts of the world, they may remain so for quite a while.

Whether they turn out to be truly endemic or not, it is indisputable that the organisms in the pond were “endangered by human activities”. In 2010, as part of an art project, somebody filled it in with earth. Imagine the alarm of researchers who had been studying the site for decades when they found out their protists had been buried! It was this event that prompted investigators to call for protection, resulting in the restoration of the pond to its previous condition and the creation of a buffer zone around it:

Buffer zone around Krauthügel Pond

Protected zone around Krauthügel Pond

And that brings us to the second reason for conserving this puddle: thanks to the work that had already been done there, it has become the “type locality” for some eighteen species (eight new species, and ten redescribed taxa). The significance of this might require a bit of explanation.

amblyodus taurus

Amblyodus taurus (click image for source)

When a biologist names a new taxon, the usual practise is to select a particular fixed specimen, or group of specimens, as the “type,” and (ideally) to deposit that specimen in a permanent collection somewhere, available to other researchers.  This provides a permanent concrete reference, so there can be no ambiguity about what we really mean when we say Utricularia floridana (a species of carnivorous plant), or Amblyodus (a genus of beetle).  If need be, we can point to a certain bug on skewered on a certain pin and say, “There! Amblyodus means that.”

The site at which the type specimen was collected becomes the “type locality,” where one might expect to find others of the same breed.  That locality is especially important to protist taxonomists. Protists are small and fragile, and fixed type specimens of older named organisms are rarely available.  Even when permanent slides exist, they can be lost, or simply deteriorate over time.  If we know the type location where our guys were originally found, we can go look for them there. In theory. But if the place at which the work was done has been drained or paved, and no type material exists, the identities of the species found there can be lost in taxonomic noise.

What is being conserved at Krauthügel is, at least in part, the scholarly work that has already been done there.  It is a body of acquired biological knowledge, and not just the organisms themselves, that is being protected.  From this point of view, environmental conservation can be similar to task that museum and art conservators do, preserving the best products of human effort for future generations.

Where does that leave all the ponds that haven’t been, and likely never will be, studied?  In spring, when I drive through the countryside where I live, I see ephemeral pools by the hundreds and thousands. They flash by in the car window, mile after mile: beaver ponds, ditches, mill pools, flood plains, and wide shallow puddles in fields where cows dip their muzzles and drop their nutritious poops. Some will have less protist diversity than Krauthügel, a few may have more, but none will ever enjoy the benign oversight of Wilhelm Foissner.

But what if more research were being done on these bodies of water–a protistologist for every puddle!–and more ponds found worthy of conservation? It is not clear where that road goes. If the Krauthügel initiative stirred up any controversy in Salzburg, there’s no record of it in the article, or the press release, but it’s not hard to anticipate the kind of pushback we’d see if similar initiatives were tried here.  Attempts to control the use of private land arouse deep and incredibly long-lived resentments.  Twenty-five years after efforts to conserve habitat for the Northern Spotted Owl in the PNW, anti-environmentalists are still seething and sneering. In some circles, the words “spotted owl” have become a kind of shorthand for “meddlesome tree-hugging morons who place a higher value on a stupid bird than the lives and livelihoods of hardworking humans.” Imagine the volcano of outrage that might erupt over the mandated protection of a one-celled organism! We would never hear the end of it.

All the same, the idea of protecting protist habitat has a lot of appeal for me.  Down the road from my house in the Gatineau hills, there’s a group of ephemeral ponds where I like to gather samples. Within a few years, they will almost certainly be filled in, as the land is subdivided for new housing. I’ve watched those ponds for several seasons, and hate the idea of losing their amazing microscopic diversity. If, as is statistically probable, they contain a few new species, there might even be grounds for conservation. However, it is pretty certain that the bulldozers will get to any new organisms before I gain the competence and resources to find and describe them.

Still,  I find it a little comforting to remind myself of the very different scale and speed of life at the microscopic level. When you are a hundred microns long, from tip to tail, a puddle is a lake, and a pond is an ocean. An hour is a year!

In a few days, a rain-filled tire rut can burst into startling diversity, like a miniature coral reef. Species bloom in quick succession, replacing and displacing one another. Each one changes the chemistry, light-permeability and nutrient load of the water, conditioning the environment to suit certain organisms, all of whom, in turn, will alter the water around them. Accidents of geography (a floating leaf,  a ball of dung) make opportunities for some organisms, and extinguish all hope for others. Things progress quickly. If you return to the tire-rut every day and follow its progress with the help of a microscope, it can seem like looking at a time-lapse film. In the “big” world, environments change in much the same way, but over longer periods of time: forests encroach on prairies, then recede; wetlands take shape, silt up and vanish; animals come and go.  At the microscopic level, shifts in populations may happen in hours, instead of years, and change is unremitting. “Ecological balance” is never achieved: things happen, then more things happen. Some species flourish, others fade from view. Then one day the hot sun dries it all up, and the little creatures climb back into their resting cysts, as their habitat reverts to grass.

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References:

Cotterill, Fenton PD, et al. “Conservation of Protists: The Krauthügel Pond in Austria.” Diversity 5.2 (2013): 374-392.