Taxonomy – It Came from the Pond

A 200-year nomenclatural trainwreck

Difflugia, Taxonomy, Testate amoebae 5 Responses »

Nov 212024

*Difflugia pyriformis* from Chisasibi, QC (or so I say)

On a recent trip to the eastern coast of James Bay, I collected large numbers of testate amoebae that, by morphological criteria, belong to various species in the genus Difflugia. I’ve spent some time making portraits of them, measuring them, and dropping live ones in little vials of guanidinium thiocyanate in the hope of eventually getting a gene sequence from them. My plan is to figure out how some of these Difflugia-shaped things relate to one another, and to other Difflugia-shaped things that have already been sequenced, and then to compare all of these to certain Difflugia-shaped things that have been described in the past.

But before getting to that, I needed to get up to speed on the tangled taxonomic history of the Difflugia, the oldest genus in Arcellinida. It’s a task that calls for a certain kind of person, one who enjoys rummaging through centuries-old texts, and squinting at bad scans of fading illustrations, to settle really small arguments about really small creatures.

In other words: a pedant.

I’ll need to draw on deep reserves of pedantry, here. I won’t apologize for that, but I can include a warning, at least: to anyone not already obsessed with the subject–as I am, obviously–it will be dull. Numbingly, crushingly, excruciatingly dull.

The beginning

Sometime in the early 1800s, a French microscopist named Léon Leclerc encountered a creature like none that had ever been described. It was no bigger than a tenth of a French “ligne”, which would make it about 226 micrometres long. It lived in a little shell covered with grains of sand. From the mouth of this “têt” (test) it extended “long arms of a beautiful milky white” which varied constantly in size, number and organization.

At first he took it for a small mollusc, and tried unsuccessfully to find its eyes. He also tried to see cilia, like those found in other “animalcules,” but it had none. In subsequent investigations, he encountered thousands more of them in a variety of types, but he could never make out any internal organs or determine what food they ate.

Because of the “imperfection” of his observations, he waited a long time to announce his discovery to the world. Finally, in 1816¹, at the urging of the horticulturalist Louis Bosc (best known, maybe, for the sweet pear that bears his name), he published a short article describing a new genus of “amorphous polyp.” He called it “la Difflugie,” or “Difflugia.”

This was the origin of a classificatory hairball that taxonomists are still trying to cough up, more than two hundred years later.

Illustrations of “La Difflugie”, from Leclerc, 1816.

In his article, Leclerc included six figures depicting what appear to be three species of arcellinid testate amoebae.² The first (labelled F. 1 and F.1a) is easily identifiable as Lesquereusia modesta, the morphospecies I discussed in my last blog post. The second (labelled F. 2 and F. 3) is roughly pear-shaped, and possibly a member of what we now call the Difflugia pyriformis complex (like the one in my SEM image, above). The third one (F. 5) is usually interpreted as Difflugia acuminata, a species that has recently been moved to another genus in a clade that branches well apart from Difflugia.

Leclerc did not name any of the species he depicted, and he did not assign a type species to his genus, as modern taxonomists are expected to do.

This lapse was remedied the following year, when the great French zoologist Lamarck added Leclerc’s Difflugia to his colossal multi-volume Histoire naturelle des animaux sans vertèbres. Lamarck proposed that the type species of the genus should be called Difflugia protæiformis. Unfortunately, he did not supply a picture or description of this new species, but simply referred to Leclerc’s “mss” (presumably, the manuscript version of the paper Leclerc published). So, which of Leclerc’s drawings is Lamarck’s D. protæiformis? The answer seems to be: all of them. His decision to combine three different forms under one name is perhaps explained by the specific epithet he chose, “protæiformis“, that is, “protean in form” (mutable, ever-changing). It is possible that the term refers not only to the perpetually shifting organism itself but also the presumed variability of its shell.

This means that, for the purposes of taxonomy, the “type species” of Difflugia is a chimeric entity consisting of three different species, two of which are no longer even included in the genus.

C.G. Ehrenberg

*Difflugia proteiformis* as depicted by
Ehrenberg in 1838

In 1830, the great German zoologist C. G. Ehrenberg incorporated Difflugia into his classification of “infusion animals”, placing it in the group of shelled “Schmelzthierchen” (“melt animals”) he called Arcellina. At first, he recognized just two members of the genus: the type species, which he spelled “D. proteiformis” (dropping the ligature Lamarck had included in the name), and another one that had a long shell equipped with a spike, which he called “the pointed melt animal,” Difflugia acuminata.³ Both species were given full descriptions in his magnum opus of 1838.

The various forms he identifies as proteiformis in that later work are all quite different from any of the Difflugia in Leclerc’s illustrations. They are most similar to Leclerc’s F. 2,3 but to modern eyes none of them look like the same species. On the figure to the left, the one he labelled “I. c” has a lobed aperture, so it is likely a species of Netzelia, such as N. lobostoma or N. gramen. The ones labelled “I.a” and “I.b” have an overall shape and texture that suggests Netzelia tuberculata, to me. The other two (“l.d” and “l.e”) are unrecognizable, but both much smaller, and rather different from one another.

So, Ehrenberg’s proteiformis, like Leclerc’s, appears to be a chimeric entity, combining three or four morphotypes under one name.

Some *Schmelzthierchen* from Ehrenberg (1838). *Difflugia acuminata* (lower right, labelled III), and *Difflugia oblonga* (top, labelled II a-d). (The tiny shells on the lower left are a euglyphid currently known as *Trinema enchelys*).

The second species he found and named in 1830, Difflugia acuminata (the large, pointed shell labelled III in the drawing to the right), was probably related to the one Leclerc depicted in his third drawing (Pl. 17, Fig. 5). In 1838, Ehrenberg added another large species to the genus, which he called Difflugia oblonga (II a-d in the illustration to the right).

Both of these two species would play a role in the decades of taxonomic confusion that would ensue.

Maximilian Perty

*Difflugia proteiformis*, from Perty (1852). It appears to be *Lesquereusia spiralis*.

The next to revise the genus was Maximilian Perty, professor of zoology at Bern University in Switzerland. In 1849, Perty published a survey of the microscopic organisms of the Italian Swiss Alps. Among the species of Difflugia he found in alpine lakes, he mentions “D. Proteus“, probably an idiosyncratic rendering of D. proteiformis. Three years later, he published an illustration of that species. The specimen he depicts is one he considered a “Monstrosität”, a deformity of Difflugia proteiformis. It is easily recognized as the notably non-monstrous species we call Lesquereusia spiralis.

In addition, he names two new species: Difflugia acaulis (a lanceolate shell, which he would later describe as a variety of Ehrenberg’s D. acuminata); and one to which he gives the name Difflugia pyriformis. The latter is described by Perty as “pear-shaped”, with its narrower end toward the mouth and a texture like that of D. proteiformis Ehrenberg. Perty gives its size as 1/7-1/5”’.⁴

*Difflugia pyriformis*, from Perty (1852)

The unit he is using there is the “line”, the exact size of which varies from one European locality to the next. It is usually one twelfth of whatever length the local inch happened to be. We don’t know exactly what version of the unit Perty was using, but a reasonable guess would be the Swiss line, which is the same as the French one, equal to 2.26 mm. So, Perty’s pyriformis probably ranged from 323 μm to 452 μm in length.

It’s a big shell!

This is worth emphasizing, because later authors would conflate the species with Ehrenberg’s D. oblonga. That species, however, was only 1/18th of a line long, which comes to somewhere between 111 and 125 μm (depending on whether he was using the Prussian, the Viennese or the French line).⁵ So, Perty’s new species, though somewhat similar in shape to Ehrenberg’s, is about three times bigger. Yet, despite the size disparity, even Perty himself seems to have some difficulty differentiating the two species, expressing doubts about eight specimens he had gathered in Switzerland’s Rosenlaui gorge and identified as D. oblonga: “Could they have belonged to my D. pyriformis?” (my translation).⁶

Joseph Leidy

The next major figure on our Mount Rushmore of Difflugia taxonomy is Joseph Leidy, author of the most beautiful book ever written about amoebae: Fresh-water Rhizopods of North America (1879). Leidy puts his finger on the problem with the type species. “The name of Difflugia proteiformis,” he reminds us, “is exceedingly indefinite in its application.”

For some of his contemporaries, the “indefinite application” of the name was actually the point. It reflected what they took to be the extreme variability of that species. One of them, the cranky and quarrelsome George Charles Wallich, took this notion to its limit, arguing that that all the named varieties of Difflugia–and those of Arcella, too, as well as Centropyxis, Nebela, Quadrulella and some others–were just different forms of Difflugia proteiformis, and that variations in their shells were only the result of “the ever-changing fluctuations of the medium by which the organisms are surrounded”. ⁷

Leidy–who was himself a taxonomic “lumper”, by modern standards–concedes that the Difflugia shell was “very variable in shape”, but sorts these variations into 10 distinct species. He does what he can to disentangle proteiformis from some of the forms to which it had already been attached.

Leidy recognizes that Lamarck’s species name did not apply to any one of Leclerc’s drawings, but to all of them together “without discrimination”; and further, that all three could be identified with species that had been described by later authors under other names: D. spiralis, D. acuminata and D. pyriformis sensu Perty.

*Difflugia globulosa* from Dujardin, 1837

Additionally, he recognized that Ehrenberg’s proteiformis was something different from any of those in Leclerc’s drawings. He considers it a synonym of another Difflugia, a balloon-shaped arcellinid with a round aperture first described by Felix Dujardin, in 1837, as D. globulosa. Dujardin himself clearly distinguished his species from D. proteiformis, since the latter had a shell “covered with little grains of sand,” whereas his globulosa was smooth.⁸ However, Leidy’s version of globulosa–based on specimens he had gathered in North America–had a sand-covered shell, so it could be comfortably synonymized with Ehrenberg’s proteiformis, regardless of whether it was the same as Dujardin’s.⁹

But, lest anyone think the case had been solved, he introduced another twist to the plot. In a later section of his book, Leidy invokes a different candidate for Ehrenberg’s proteiformis, a species with a three-lobed aperture which he himself had described under the name Difflugia lobostoma. Of that species, he writes: “As ordinarily seen, it bears so close a resemblance with the corresponding views of Difflugia proteiformis, as described and figured by Ehrenberg, that it may not only be readily taken for the same, but I have suspected that Ehrenberg may have actually had this animal under observation when he described D. proteiformis.”

Leidy suspects his own lobostoma to be identical with a species that had been described two decades earlier by H. J. Carter, as Difflugia tricuspis, but he rejects that name–despite its priority–because “tricuspis” implies that this species could only have three lobes in its aperture, whereas Leidy had determined that it could have as many as six.¹⁰

Whatever name we assign to it, Leidy’s Difflugia lobostoma, strikes me as a reasonable candidate for at least one of Ehrenberg’s proteiformis illustrations. As I mentioned above, Ehrenberg’s Fig. Ic clearly shows a lobed aperture.¹¹ However, the size Ehrenberg gives (100 μm) falls in a grey zone between Netzelia lobostoma and Netzelia gramen. In any case, as I pointed out before, there’s no particular reason to feel sure that Ehrenberg’s illustrations all depict the same species.

Eugène Penard & the pyriformis problem

In 1902, the genus Difflugia went pear-shaped, when Eugène Penard reassigned Lamarck’s type species to D. pyriformis Perty, 1852. That placement–based only on Leclerc’s Fig. 2 & Fig. 3–is arguably more plausible than Leidy’s (D. globulosa), but it steers the taxonomy directly into yet another collision.

*Difflugia pyriformis* “habitual forms”. Penard (1902)

In 1909, in the second volume of their British Freshwater Rhizopoda, James Cash and his assistant John Hopkinson conducted an exhaustive literature review of Difflugia pyriformis Perty (1852) and Difflugia oblonga Ehrenberg (1838). The bibliographic effort was magisterial–their references fill more than three closely-packed pages–and their final judgment was expressed very simply: the two species were one, and since Ehrenberg’s had priority they should be collapsed together under the name he used. Henceforth, everything known D. pyriformis would be called oblonga.

As for the type species, our old friend “Difflugia proteiformis,” that presented a problem. If it were retained as D. pyriformis, that would make it a synonym of D. oblonga, in which case Ehrenberg’s two species–and all the observations that had ever been referred to them–would be compressed together into one misshapen lump. However, Ehrenberg’s oblonga and proteiformis, according to Cash and Hopkinsons, could not be accepted as synonyms. Therefore, they wrote, “the safest course now is to discard the name proteiformis altogether.”

The proposed synonymy of pyriformis and oblonga made it a remarkably variable (one might even say “protean”!) species. As Ferry Siemensma has pointed out, in a very useful discussion on the D. oblonga page of his website, there is a rather spectacular size difference between the species Ehrenberg illustrated and the pyriformis morphotype as it is generally understood. It’s the kind of difference that is easily overlooked when we are looking only at illustrations and photos in published sources, so Ferry dramatizes it for us by providing a properly scaled picture of Ehrenberg’s shell alongside a group of shells illustrated in Chardez (1967) as varieties of D. oblonga:

Ehrenberg’s *Difflugia oblonga* (lower left, indicated by the red arrow) compared to some shells assigned to the same species by Chardez. Source: Microworld: world of amoeboid organisms

If you were to encounter a group like this in your microscope would you consider the little straight-sided shell on the left to be a member of the same morphospecies as the large bottle-shaped ones on the right?

I would not.

However, that’s a subjective judgment. To prove that they truly are different would require a better method than my usual one of peering at them thoughtfully while stroking my chin.

Palaeontology weighs in

When Cash and Hopkinson recommended discarding proteiformis, they just formalized what taxonomists had already been doing: ignoring an incoherent taxon. For the purposes of stable classification, though, this was not ideal.

In taxonomy, the type species of a genus has a special status: it’s the indispensable thing to which the genus name refers. Other species can be removed from the genus, but the type species is permanently tied to it. Without its type species, the validity of the genus itself comes into question.

Helen Tappan and Alfred R. Loeblich. Source: Journal of Foraminiferal Research

In 1964, this situation was addressed by two American micropalaeontologists (who happened to be married to one another), Alfred. R. Loeblich and Helen Tappan. By that time, Difflugia and its 300 nominal species had been drifting along without a clear type species for nearly five decades. As others had before, Loeblich and Tappan noted that Lamarck had never specified which of Leclerc’s drawings should represent the type of the species. So, as Leidy and Penard had also done, they picked one of Leclerc’s images to fill this position. The illustration Loeblich and Tappan chose was Leclerc’s Fig. 5, the one with a pointed fundus, which is usually regarded as a specimen of Ehrenberg’s D. acuminata.

Their reason for picking Fig. 5 was interesting, and (I think) novel. In their interpretation, all the other images Leclerc had drawn (Figs. 1-4) were depictions of the same organism, the one now known as Lesquereusia. As they saw it, the drawings that look like “pyriformis” (Figs. 2 and 3) were simply “edge views” of the first two. So, by their reckoning, Leclerc’s Fig. 5 was the only one of his drawings that was still “unquestionably Difflugia as generally understood.”

They formally declared this image to represent the type species of the genus: “As no lectotype has yet been designated, we here designate as lectotype of D. protoeiformis the specimen illustrated on Pl. 17 Fig. 5 of Leclerc.”

Their spelling of the species name was a simple mistake–they seem to have misread the aesc ligature (æ) used by Lamarck as an oethel (œ). Later authors would restore Lamarck’s original spelling (but with no ligature, since that is forbidden under ICZN rules).

Their term “lectotype” refers to the use of an illustration to serve as the “name-bearing type” of the species. In taxonomy, every species is expected to be based on a single representative specimen. Ideally, this would be a material object, a preserved specimen which acts as a permanent reference point for the taxon. For obvious reasons, physically preserved “holotypes” of microscopic species (especially older ones) are often unavailable. In such cases, the rules of nomenclature allow an illustration or photograph to serve the same purpose.

*Difflugia protaeiformis* Lamarck, 1816? Stacked image by Bruce Taylor.

Their choice of Leclerc’s fifth figure as the name-bearing type of Difflugia meant that Ehrenberg’s Difflugia acuminata would now be a junior synonym of Difflugia protaeiformis. A lot of work had already been done on that morphotype under Ehrenberg’s name, so it was a bit awkward. And, of course, the resurrection of D. protaeiformis risked reviving the taxonomic chaos that had swirled around that name from the beginning.

By and large, researchers who have accepted Loeblich and Tappan’s lectotype have come from the community of palaeontologists and palaeolimnologists, many of whom use fossil testate amoebae as indicators of ecological conditions in ancient bodies of water. Those who come to the subject from protistology, eukaryotic microbiology, cell biology, etc., have generally rejected or ignored it.

In 1988, Ogden & Ellison questioned the validity of Loeblich and Tappan’s lectotype, on the basis of their personal communication with a colleague identified as “Merifield” who argued that, as he interpreted the International Code of Zoological Nomenclature (ICZN), Article 74b, the image that had been chosen for their lectotype was “invalid and, as a consequence, should be rejected.” They went on to promise that the matter would soon be brought before the ICZN: “A complete justification of this opinion is in preparation (Merifield, in prep.) for submission to the Commission, in which it is hoped to designate a more correct type species for Difflugia.”

I don’t know what became of this plan, but if a “more correct type species” was ever designated, I can find no reference to it.

Deconstructing Difflugia, 2022

Since that episode, Difflugia systematics has moved on. Between 2012 and 2015, in a series of three papers, Yuri Mazei and Alan Warren undertook an ambitious review of the genus, based on shells in collections left by Eugene Penard and Colin G. Ogden. They left Loeblich and Tappan out of the discussion, and allowed the question of the type species to remain unsettled, but that made little difference because by this time arcellinid taxonomy was already well into the era of molecular phylogenetics.

In 2022, an all-star team of testate amoeba specialists headed by Ruben González-Miguéns investigated some putative members of Difflugia by looking at certain mitochondrial and nuclear genes. Their findings confirmed earlier indications that the old genus was a polyphyletic grouping, which is to say that some of its members are more closely related to arcellinids in other groups than they are to each other.

As a first step toward recovering all the monophyletic groups currently buried in Difflugia, they carved some new taxa from the old genus. One is a single-species genus they named Golemanskia, in honor of a colleague. The other comprises a handful of “Difflugia” species, mostly with long and/or pointy shells. For that one they came up with a jaunty portmanteau, combining “cylindrical” and “Difflugia“: Cylindrifflugia.

A phylogenetic tree based on sequences of the mitochondrial NADH gene (trees based on COI and SSU genes not shown here)

Among the species they transferred to Cylindrifflugia was none other than Leclerc’s “fig. 5”, Difflugia acuminata. Consequently, the oldest “surviving” member of Difflugia (and, according to some, its type species) is now in a separate genus. The genus itself now resides in the new infraorder Cylindrothecina, a group delimited “by its specific sequences of the mitochondrial and nuclear DNA markers (COI, NADH and SSU) and by its phylogenetic placement.”

Specimens identified as D. pyriformis, nodosa and oblonga group well apart from Cylindrifflugia, and are retained in the infraorder Longithecina where, presumably, they will make up the core difflugiids in future investigations, as more taxa are carved from the old genus.

At some point, some brave taxonomist will have to propose a type species for the ones that remain.

Notes

The date is usually given as 1815, but that was corrected by Loeblich and Tappan, in 1964. The volume in which Leclerc’s article appears carries the date 1815, but includes publications issued over two years. ↩︎
However, Loeblich and Tappan read the first four images as belonging to a single species, as I’ll explain further on. ↩︎
Difflugia acuminata was discovered as Ehrenberg’s book of 1830 was in already in press, and he gives little information about it, though he does specify that the creature “disdains coloured food.” ↩︎
The size range is taken from his book of 1852. In the original description, in 1849, he gives a slightly narrower range of 1/6-1/5”’. ↩︎
This has been pointed out by Ferry Siemensma on his website. ↩︎
Mazei and Warren misread this passage, taking it to mean that Perty is questioning the validity of Ehrenberg’s oblonga. It’s a puzzling conjecture, since oblonga clearly had priority and Perty would not have thought his new name would supercede the older one. He doesn’t appear to have any doubts about the validity of either oblonga or his pyriformis, but just doesn’t know where to assign his Rosenlaui specimens. ↩︎
For clarity, I’m mostly omitting Wallich’s contributions, but they’re quite interesting. He published a detailed revision of the Difflugidae in 1864, seemingly based on his belief that shell shapes grow and change as amoebae mature. From this starting place, he argues that all the named varieties of Difflugia–and those of Arcella, too, as well as all the amoebae we now place in Centropyxis, Nebela, Quadrulella etc.–were a single species, and that variations in the shells were only the result of “the ever-changing fluctuations of the medium by which the organisms are surrounded”. There is much to be said about this unusual gentleman, but I’ll reserve it for another day. His ideas about amoeboid classification were not very influential. ↩︎
Dujardin’s description of D. proteiformis: “An[imale] à coque noirâtre ou verdâtre, globuleuse ou ovoïde, recouverte de petits grains de sable. — Longueur 0,043 à 0,112.” And his description of D. globulosa: “An[imale] à coque brune, globuleuse ou ovoïde , lisse. — Longueur 0,10 à 0,25.” ↩︎
I should point out another uncomfortable fact, which is that neither Dujardin’s D. globulosa nor the one depicted by Leidy actually resemble the organism conventionally given that name in modern work. In recent work, the name D. globulosa is applied to species that are nearly spherical, with a much wider aperture than we see in Dujardin’s image of 1837. The modern idea of globulosa resembles the arcellinid Wallich recorded as Difflugia globularis, which some taxonomist still differentiate from globulosa. Leidy takes Wallich’s name to be an erroneous spelling of D. globulosa, and Wallich himself does not dispute that claim in his furiously detailed critique of Leidy’s book. See: “Critical Observation on Joseph Leidy’s Fresh-water Rhizopods of North America” (1885). Ogden examined Wallich’s annotated copy of Leidy, and reported that Wallich had written “quite true, it was a mistake” in the margins, next to Leidy’s comments (Ogden, 1988). ↩︎
Under the rules that govern nomenclature, Leidy’s D. lobostoma is really a junior synonym of D. tricuspis Carter, 1856 (currently, Netzelia lobostoma). However, Leidy’s name is the one everybody uses, and…well, the taxonomy is already complicated enough! ↩︎
Cash, Wailes and Hopkinson agree with this interpretation, saying that Ehrenberg’s proteiformis was “in all probability one of the species with a lobate mouth (e.g. D. lobostoma Leidy).” ↩︎

References: Click Here

A new species named for Ferry Siemensma

Amoebae, Chlamydophryidae, Ferry Siemensma, Taxonomy No Responses »

Nov 122016

After studying amoeboid organisms for several decades–observing them in the field, publishing articles about them, and developing his wonderfully detailed website devoted to the little shapeshifters—Ferry Siemensma now has an amoeba he can call his own. The organism, discovered by researchers in a small greenhouse pond at the university of Cologne, is Lecythium siemensmai, a cercozoan amoeboid that lives inside a flexible, secreted transparent “theca”. It looks like this:

Source: http://www.sciencedirect.com/science/article/pii/S1434461016300438

The new species, is described, along with several others, in a complete revision of the genus Lecythium, recently published by Kenneth Dumack and two colleagues at Cologne. The genus itself is fairly old—it was erected by Richard Hertwig and E. Lesser in 1874—but it has been a very long time since taxonomists have paid any attention to its composition. Many organisms that properly belong in the group have been misplaced in other genera, such as Gromia, Trinema and Pamphagus. The latter has been recognized since 1915 as an invalid group (the name properly belongs to a genus of grasshoppers), but it is a mark of the neglect into which amoeboid taxonomy has fallen that a Google search on “pamphagus amoeba’’ turns up dozens of modern micrographs and videos of cells identified as belonging to a group that was formally abandoned over a hundred years ago. It is a tribute to the great amoebologists of the past that their work still casts such a long shadow. It is also a reminder that revisions like this one by Dumack et al. are urgently needed.

The paper, charmingly titled “A Bowl with Marbles” (a reference, presumably, to the glassy, round shape of the organism’s soft theca), uses molecular phylogeny to establish the genus as a well-defined clade within Tectofilosida (a rhizarian group whose organic shells lack the siliceous scales secreted by better-known filose amoebae like Euglypha and Assulina). In the section on taxonomy, the authors deftly untangle a few historic hairballs; for instance, tracing the relationship of their Lecythium spinosum to antecedents like Trinema spinosum, Plagiophrys armatus and Pamphagus armatus. Finally, they provide a visual key to the group, featuring clear illustrations and helpful diagnostic clues. For this genus, at least, they have built a convenient foot-bridge between phylogeny and field identification.

Congratulations to Ferry, and to the researchers at Cologne, all of whom are doing the kind of work that could coax future researchers back to the field.

REFERENCES:

• Dumack, Kenneth, Christina Baumann, and Michael Bonkowski. “A Bowl with Marbles: Revision of the Thecate Amoeba Genus Lecythium (Chlamydophryidae, Tectofilosida, Cercozoa, Rhizaria) Including a Description of Four New Species and an Identification Key.” Protist 167.5 (2016): 440-459.

• Hertwig, Richard, and E. Lesser. “Ueber Rhizopoden und denselben nahestehende Organismen.” Arch. Mikr. Anat 10.1874 (1874): 35-243.

Meet the Protistologist 2: an interview with David J. Patterson

Biodiversity, Meet the Protistologist, Taxonomy 7 Responses »

Mar 262014

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.

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”).

Another 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, 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.

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 (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.

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?

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.