Monday, April 14, 2014

This is not a post about nomenclature.

This is not a post about insects, or insect genitalia, or another round in the Vandal of the Calypterates series (but the next one of that is coming, I promise!).

This is a deeply personal thing I am going to talk about, which is entirely uncharacteristic for me and what I like to post here. Sure, I get rant-y about ICZNerdery, or the latest round of "the Naturalists are Dying Out". These are all par for the course, have been since the beginning of this blog. I share my love of, say, weird caddisfly life histories and get excited about it, because that's something I enjoy doing. I try to keep more personal things off this blog because (a) I don't especially enjoy sharing personal parts of my life, (b) the name is Trichopterology, not Facebook 2.0, and (3) the personal stuff is none of your business. But I feel this is important, so I'm breaking the rules.

This is going to be a post about transpeople in science and academia. Because I'm a transwoman.

I realize this will be a shock to some people. Other people will share knowing smiles. The majority of the academics will not care, and that is the point of this post: being trans in academia, at least in the biological sciences, seems to be becoming a non-issue. And the more visible transpeople are, the more of a non-issue it will become. 

When I came out to my first colleague here at Wright State last year, I was terrified. I'm not going to repeat standard introductory conversations on transpeople and gender identity, there are a multitude of primers out there in the InterWebz. Just Google it. What I will say is that transpeople are not exactly treated well by society in general, and our tendency is to expect the worse of any social situation in which we out ourselves. 

To my surprise and relief, my colleague was accepting and has been a huge ally. I told more people I felt I could trust, and not one of them rejected me. Some of them had guessed ahead of time. Others were excited for me. The majority were interested, supportive, and quite frankly, treated me like normal. 

When I made my gender identity public to the department in early March, my anxiety was decreasing. Graduate students and faculty, with few exceptions, had positive reactions. Many knew or knew of Joan Roughgarden, an evolutionary biologist who transitioned in the late nineties. Some had personal experiences with trans or other queer people. I found friendships had actually strengthened due to my trust. 

Perhaps I live a charmed life, that my experience is special, not normal. My university includes gender identity and expression under the non-discrimination clause, which means that faculty and staff have to respect my identity, regardless of their personal feelings. My department is a close knit group of open minded ecologists and evolutionary biologists with a wide array of life experiences. In the unlikely event I am ever harassed, the university will respond quickly to fix the problem. Many transpeople cannot claim the same about their university or department. 

Yet, I cannot see how my experience is completely unique. One of the most wonderful results of my coming out was being invited to a small panel by women faculty for women graduate students. When I asked about my opportunities for finding a job as a transwoman, the faculty members responded that I shouldn't worry about it, that the real issue is the community surrounding the university, and not the university itself. I may not want to live somewhere due to the hostility of the college town, but the university should be a non-issue. These things are improving.

The recent "Queer in STEM" survey suggests that this improvement comes from visibility. When queer people are out and visible in university departments, they become role models and create an environment which makes other queer people, including graduate students, feel more comfortable and welcome. It's so easy to focus on the negative aspects of my situation. Sometimes I feel my transition is selfish, that I am "creating drama" by asking people to change their pronoun and name usage, that I am making things more difficult not only for myself but also for other people. But I also feel that by being visible I am showing other students that they don't have to feel anxious about their identities. I can be that role model. I can relay my positive experiences. In the words of the Trevor Project, "It gets better". It is getting better.

Thanks to Morgan Jackson for his advice and encouragement, and to this post by Alex Bond for getting the brain juices flowing. Stay tuned for normal programming.

Monday, January 20, 2014

CHT Townsend, Vandal of the Calypterates. Part II.

When we left off in Part I, John Merton Aldrich had just written some mixed comments about Townsend's work before 1905. 

     At this point, it's necessary to skip to an article 20 years later. Literature trains are often hard to follow, especially in the old literature. But we can see the events before 1925 play out through Townsend's eyes, in his inflammatory piece "The Inside History of North American Myiology". Myiology being the term he coins for the study of calypterate, or muscoid, flies. He writes,

"The history of this subject in the United States has unfortunately been characterized by a petty spirit of rivalry and jealousy for the past three decades. This, perhaps the most difficult subject as regards taxonomy, meriting on this very account the most concerted and amicable relations among its students, has met with the exact opposite during its development in North America."
     The entire paper is written in the third person, as if Townsend's history is being recounted by someone else. Another testament to his ego and arrogance.

      Townsend's history begins with a short list of insect taxonomists leading up to 1888, saying that "thus far there was no spirit of rivalry or jealousy on this side of the Atlantic." At that time he was a clerical assistant to C.V Riley in the Bureau of  Entomology, Washington D.C. He was very much interested in beetles and true bugs, but not true flies (Diptera). However, at the insistence of his supervisor, he took up work on the group. Later he was "grateful, for no other possible group of organisms
could have proved so fecund of interest in his [Townsend's] eyes, considered from all points of view." In 1891 he left D.C. for a university job in New Mexico. Evenhuis suggests in his biography that the glowing recommendations Townsend received from Riley may have been an early indication of his difficultness, that "Riley wanted him out of D.C."

     Townsend's first direct criticism is not of Aldrich, but of a contemporary, prolific, and recently deceased taxonomist, Daniel William Coquillett (1856-1911). Townsend writes that Coquillett had an interest in calypterate flies but

"little opportunity to indulge his desire for study of the subject. He chafed under the restriction and developed a bitter hatred of Townsend and his work; a hatred which he nursed diligently until his death, and which prohibited him even from conversing with Townsend except under circumstances of the direst necessity." 

     He claims that Coquillett's hatred was made clear in the 1897 "Revision of the Tachinidae of America North of Mexico", where Coquillett synonymized most of Townsend's genera with earlier names. This "hatred" seems to be a deep reading of Coquillett's unwillingness to correspond with Townsend, as the "Revision" does not have any spiteful comments that I can see. Yet Townsend takes a victorious view of the situation, stating "[Coquillett's] pronouncements, like the whole fabric of his work, are falling apart and away as investigation progresses in the groups he treated." Townsend claims,

"During all of this time and up to the last, Townsend harbored no animosity toward Coquillett and would have been glad at any time to converse with him on muscoid work, but found him so unapproachable that he would not even answer questions couched in the most courteous terms and offered in the most friendly spirit. The animosity of Coquillett brought a handful of animosities in its train."

     The first of these "animosities" is John Merton Aldrich. As noted in Part I, Aldrich's Catalogue has mixed comments about Townsend, both praising him for his species descriptions and chastising him for his strict following of Brauer and Bergenstaumm genera. Townsend condemned Aldrich for strictly following Coquillett's revision, calling it a "fatal mistake", that the "manifold errors" and ridicule towards Townsend were so extreme that "he felt he could not gracefully retract after [Townsend] began to point out in a wholly impartial manner the errors that had been perpetuated in the catalogue." This must have been a private correspondence, as Townsend did not publish his comments at the time.

     In 1908, the dipterist Samuel Wendell Williston published the third edition of his "Manual of North American Diptera". He had contracted Townsend for help with the Tachinidae, as Coquillett was unwilling, who took the opportunity to describe a few new genera, as he was wont to do. The same year, Townsend published "The Taxonomy of the Muscoidean Flies". In this work he quotes Williston on tachinids:

"We yet know very little about individual variation in this family, or the real value of many characters now used. The absence or presence of a bristle may be found to represent a group of species, but we should first learn how constant the character is in species. * * * Seriously, is not the stock of Tachinid genera significantly large for the present? Would it not be better to study species more before making every trivial character the basis for a new genus? --Insect life, vol. v (1892-93), pg. 238-40."

     To that, I say "hear hear!" But to Townsend, it was motivation to have a discussion on "intermediates" and "intergradants" (forms that connect genera and species, respectively). He used the abundance of intermediate forms as justification to devalue the rank of genus, writing,

"The only possibility of successfully systematizing the superfamily [tachinids, under his system], so that its myriads of forms can be designated definitely by name, lies in the recognition of genera founded upon comparatively slight characters -- slight compared with those recognized as the standard in the older and less specialized superfamilies."

     This was not quite the concept of a "natural genus" from his later years, but it does shed light onto his massive output of generic names in tachinid flies, and how he justified it at the time.

     Aldrich was undoubtedly displeased with this continued taxonomic vandalism. His growing opinions of Townsend became quite clear in his 1909 review of Williston's Manual. He writes of Townsend's involvement:

"Dr. Williston, wishing the criticism of a specialist on this difficult group, and being unable to secure the assistance of Mr. Coquillett, asked Mr. C. H. T. Townsend to prepare notes on the figures. This was unfortunate, as Mr. Townsend's ideas of genera are extremely radical; it naturally happened that his notes only serve to confuse the subject. He, however, seized the opportunity to erect a few new genera on the figures, which was the more out of place and uncalled for since he promised fuller descriptions in a forthcoming paper. Would that he had reserved his adumbrations in their entirety!"

     Later, Townsend would consider these "acrid remarks" the "birth of a second bitter hatred" towards himself. The second after Coquillett, soon to be followed by a third.

Continued in Part III.

Monday, January 13, 2014

CHT Townsend, Vandal of the Calypterates. Part I.

I've received a lot of feedback about my post about Call to Comments. Most of it has been considerate and helpful. There was one case of a sockpuppet by a certain someone, but it's no matter.

What does bother me is it seems like people are interpreting the post to be about the Spracklandus case when it isn't. I used the background of that case as an example, a dispute containing both bad taxonomy and thrown insults, something which has been happening since the beginning of nomenclature. I also used it because I find nomenclature fascinating, to the point where I lay away at night thinking about the ins and outs of the Code. And, because I love taxonomy, and history, and because the recentness of this case meant it was well cataloged. 

But I could have used any number of historical disputes, including the focus of this series, Charles Henry Tyler Townsend, or CHT Townsend for short.

I am not, unlike in Neal Evenhuis's excellent and overly kind biography of the man (found in this issue of Fly Times), going to recount Townsend's life. Instead, I'm going to focus on his controversial work with calypterate flies, and how in many ways he left things worse than when he started.

Townsend's chosen group, those true flies belonging to the monophyletic lineage Calypterata, contains common insects such as the house fly (Muscidae), flesh flies (Sarcophagidae), and blue bottle flies (Calliphoridae), as well as the less common but more horrific bot flies (Oestridae). But the most diverse calypterate group are the tachinids, estimated to be the largest group of Diptera surpassing even crane fly (Tipulidae) species numbers.

Dr. Townsend chose these flies as his specialty, particularly tachinids. By the time of his doctorate on calypterate female physiology (1914), he was pouring himself into the work that would eventually become the Manual of Myiology (1936-1941). That many volume set of keys and descriptions is still used today when dealing with the South American fauna.

Unfortunately, Townsend was unconventional or downright radical when it came to his taxonomy. Monty Wood of the Canadian National Collection, a world expert on tachinid flies, told me Townsend's work and opinions were simply an example of his ego and arrogance. The problem that set South American tachinid taxonomy back a century stem from one particular issue, his species concept, which lead to his tendency to split taxa ad infinitum.

In his history of tachinid fly classification, Jim O'Hara writes,

"The restricted genera of Townsend were based on the author’s concept of a “physiological genus”, defined as a “natural genus” comprising “all those species which can produce fertile crosses” (Townsend 1935: 38). As noted by van Emden (1945: 389–390), “the adoption of [this] principle implies the application of the generic unit to every unit considered to be a species in general zoological practice”. One can learn, explained Townsend (1935: 56), “to make a complete description of a fly genus and its genotype [type species] in one hour for one sex and an hour and a half for both sexes”. The ideal number of members within each of the categories of genus, tribe, family, suborder and order was set at five (Townsend 1935: 60–61). In practise Townsend rarely included more than one species per genus and throughout his career described 1491 genera and 1555 species (Arnaud 1958), with approximately 85% of the genera belonging to the Tachinidae."

 In other words, 95% of his genera were monospecific.

My current work with tachinids is not my first contact with Townsend's modus operandi. In one of his Insect Morphology lectures, Peter Adler of Clemson University would recount this strange methodology, saying that a difference in structure indicated a new genus, and a difference in color meant a new species. Townsend recorded all this information on index cards in a card filing system. Whenever he found something he considered new, he would reference the system, and fill out a new card. He also had a tendency to split the higher classification, leading to a grand total of 7 families and ~90 tribes of the current Tachinidae. This volume of new taxa matches what we would today consider to be taxonomic vandalism. It did not help matters that his descriptions were much like others of the day, paragraph length and lacking any illustrations. His keys, both in the Manual of Myiology and his Synopse dos generos muscoideos da regiao humida tropical da America (1927), were not much better; they are hundreds of couplets long and practically unusable, yet necessary works when wading through the vast fauna of the Neotropics.

Other tachinid workers reacted much in the same way you would expect: they synonymized names. In particular, this was a drawn out feud between Townsend and John Merton Aldrich, a prolific Diptera taxonomist and Associate Curator of Insects at the US National Museum from 1918 until his death in 1934.

It's not clear when the argument started. By the time Aldrich published his catalog of North American Diptera (1905), Townsend had published 84 papers on true flies. This list of publications fills up 6 pages of the catalog, more than any other author. He comments on one, writing, "An attempt to interpret Van der Wulp's too brief diagnoses, without the material to throw any particular light on them; an altogether superfluous piece of meddling. The changes of generic names are both uncalled for." He also calls attention to Townsend's strict following of Brauer and Bergenstaumm genera, yet praises Townsend for his species descriptions, writing, "The specific descriptions of Townsend are conscientious and faithful, and among the most recognizable of any in the family."

There were obviously no hard feelings at this point, but over the next 20 years their relationship of shared interest would become seriously strained by Townsend's public and often unprofessional reactions to Aldrich's work, and vice versa.

Continued in Part II.

Wednesday, January 8, 2014

The Impartiality Ethic.

     Among my many current projects, including a preliminary exam, I'm writing a novel. I was convinced by a colleague to join in the National Novel Writing Month goal back in November, and have managed to put nearly 20 thousand words into an original story. Since I write what I know, the story is about grad students, imposter syndrome, taxonomy, ICZNerdery, and natural history in a world where names have power. It will probably never see the light of day, but I did want to mention one thing. In the story, the idea of Universality of Names is taken very seriously. Since names have power, and the precision of that power is derived in part from universal usage, the process of naming is heavily regulated. There's even an analog of the International Commission on Zoological Nomenclature, which is both an arbitrator of disputes and a governing body. The Commission of that world polices the usage of names, to the point where people who do their work poorly are stripped from the books.

    The Commission of this world, does not.

      This is an important distinction, and lies at the heart of the matter I want to discuss. The Commission does not police names, it is solely an arbitrator of disputes. If the taxonomy of a particular paper is bad science, yet the names are otherwise available under The Code, it is not the place of the Commissioners to act upon it. That is, as things are now.

      In the latest edition of the Bulletin of Zoological Nomenclature, Commissioners Yanega and Harvey published a Call for Comments about "Taxonomic Practice and the Code". Before I dive into that, let's look at why we're talking about it in the first place. 

      Taxonomy has a history of people with an itch, an itch to name things. And not just a need to name things, but to have one's own name be associated with those things forever. It comes from the formal practice of writing the name of the author and the date of the publication after a scientific name. The term "mihi-itch" is sometimes used to describe this affliction, as mihi is Latin for "mine; of me" (see Neal Evenhuis 2008 paper for a full history of the term). And they will often let the ends justify the means (including bad taxonomy).

     This is not new (cf. the bone wars of the 19th century for an extreme example), yet the recent explosion of journals and other easy routes of publication have enabled those with this "disorder". Furthermore, there's no requirement in The Code for science of any kind. The Code is "theory-free", it makes no comments on how to do taxonomy. In the introduction of the Fourth Edition, the late W.D.L. Ride writes, "The Code refrains from infringing upon taxonomic judgement, which must not be made subject to regulation or restraint." Nor is there a requirement in The Code that nomenclatural acts be peer reviewed, a relatively new academic invention. This hands-off attitude is important because, as arbitrators, the Commissioners must remain neutral in the cases they are hearing. The Code of Ethics in Appendix A states: '7. The observation of these principles is a matter for the proper feelings and conscience of individual zoologists, and the Commission is not empowered to investigate or rule upon alleged breaches of them.' All of this means that those with the mihi-itch do unwanted things that are outside the ability of the Commission to arbitrate upon.

      The impetus for this particular discussion is a case submitted by Ramond Hoser of Australia. Hoser is a herpetologist who has become infamous in taxonomy for what Darren Naish calls "taxonomic vandalism", and what I have heard others call "taxonomic inflation", or even hyperbolize as "taxonomic terrorism". The method is simple: Produce publications with a large number of nomina nova in the hope that some of them will pay out and actually be valid. In his recent paper "The Taxon Filter", Hinrich Kaiser writes, 

"...Hoser uses the Code as a ‘name-laundering scheme’: his mass-produced names go in and ‘clean’ names come out. The more names that are put through the system, the greater is the likelihood that some will by coincidence stand if science eventually produces supporting facts. None of these names have a rigorous scientific foundation..."

     So, the overall quality of work is poor. However, as long as the new names follow the letter of the Code, the names are still available. And if a few of the names which satisfy availability end up being new to science, they're valid. In which case occurred when he happened to raise cobra (Najas) subgenera in a scoop of other taxonomists in his own self edited journal. In particular, his genus Spracklandus was valid, and not just as a potential classification scheme, but in the exact manner these other taxonomists were working to publish as subgenera. Needless to say, Wallach, Wüster, and Broadly were not please, and published their own revision of the subgenera later that year. The three authors named the subgenus Afronaja, and claimed the Hoser publication was not available under the code because it was not properly published. They write,

"Although Hoser claims the existence of a printed version of his journal, we have found evidence of only one single copy, deposited in the Australian National Library (ANL). [...] On 9 May 2009, one of us (VW) recieved printed copies of all the issues of the Australasian Journal of Herpetology. Unlike the ANL copy of Issue 7, all these issues are printed on one side only, and give the appearance of having been printed on demand at the same time: all have a pair of longitudinal white lines along the midline of the entire page: issue 1 has the lines spaced about 2 mm apart but all the other issues have the lines spaced 5 mm apart, suggesting that they were printed at the same time. These lines are not present in the ANL copy of Issue 7. All the issues received by us are bound by a single large staple in the upper, left hand corner. We conclude that the Australasian Journal of Herpetology is an online publication that fails to fulfill the requirements of Articles 8.1.3 and 8.6, any printed copies are printed on demand and therefore do not constitute published work under the provisions of Article 9.7, and the electronic versions available from Hoser's website are not published under the provisions of Article 9.8."
     To make the rest of the story short, Hoser claimed the authors were frauds, saying, "the men chose not to look in the one place that the Zoological Rules said hard copies should be sent to, namely Zoological Record". (Which makes it seem like he isn't as familiar as he considers himself, since there is no provision in The Code requiring copies to be sent to the publication Zoological Record, only a recommendation.) People are now confused about which revision to use, and cobras are, as you might guess, medically important snakes. If the journal was published hardcopy, Spracklandus is available, and Afronaja is a junior objective synonym, and invalid. If the journal was not published hardcopy, "Spracklandus" is unavailable, and Afronaja is the valid name. All of this is the subject of Case 3601 Spracklandus Hoser, 2009. 

     And whatever decision comes out of that case is irrelevant to me. Before Mr. Hoser or any of his friends descend upon my blog like locusts to grain, I work on insects, not snakes, I have no stake in this. I don't care if the subgenus is named Afronaja or Spracklandus. Whatever the Commissioners decide is fine by me. I do find Hoser's journal atrocious and taxonomic methods (or lack thereof) appalling, but my opinion on that matter is powerless. Please leave me alone, I'm just a poor grad student.

      What is relevant to me is that this case has prompted a Call for Comments by Commissioners Harvey and Yanega. This is a request for opinions from the greater community of taxonomists. The Commission receives open comments on all their cases, but this is a more general call; not about the Spracklandus case in particular, but about the historic and continued neutrality towards ethics and unwillingness to police the taxonomic community. They write,

"The question has been put before us, however, as to whether the desires of the community can compel a re-evaluation of the policy of neutrality; specifically, whether taxonomic freedom requires us to remain blind to ethical considerations, including a failure to adhere to proper standards of scientific conduct. Therefore, we seek guidance from the taxonomic community as to whether there is a perceived need for change, and we wish to solicit comments in order to ascertain a clearer picture of public opinion. We are, ultimately, at the service of the community, and if there is a consensus indicating that the community feels neutrality does not serve their needs, then we wish to be clear about it. 

[...] Basically, what we seek to know is whether the taxonomic community wants to continue dealing with these issues at their own discretion, or whether they want the Commission to be empowered to do so (or something in between); we will not do so on our own initiative."

     I love that, a perfect exposition of neutrality, and the unwillingness to wield power unless asked. The antithesis of politicians. They're asking us how they may best serve all of us. Go over and read all of it, it's short and sweet.

     So. As stated above in the bold text, I'm just a lowly grad student. They're asking for comments, but I'm not confident enough to submit my opinion to the Commission on this matter. But if I were to submit a comment, maybe it would go something like this.

     The long standing neutrality of the Commission is an important part of remaining above conflicts within the taxonomic community. A reduction in the sort of neutrality described in the Code of Ethics will mean the Commission has the possibility of becoming a 'political tool' rather than a body for impartial arbitration of conflicts. It will set a precedent in a system which is supposed to avoid making precedents. The Commissioners should continue to arbitrate only on cases brought to them, and only on conflicts covered under the Code, and should not seek out problems for which to "apply justice". Instead, taxonomists should band together in rejection of those who fail to uphold scientific ethics and good taxonomy. 

     I am a student, and I have little power. But, if I am worthy, I would hope someday to be selected to serve this community. If I am honored with that task, I would like be the sort of arbitrator described illustrated in the Call for Comments: impartial, restrained, and dedicated.

Monday, January 6, 2014

"By people who don't need them for people who can't use them."

Recently, I discovered the long awaited revision of the North American black winged fungus gnats (Sciaridae) has finally been published (Note: link is only the first page). Studia Dipterologica is a relatively obscure publications for fly nuts, so it took some digging to get a copy. In my excitement upon arrival, I scanned through the entire text, looking for the thing I was really excited about. And it's not there, there's no genus key.

A bit of background: The Manual of Nearctic Diptera remains today a masterpiece, 30 years after publication. It includes generic keys to every family of Diptera in North America, for adults and sometimes for larvae as well. And it's freely available online, too, so all the better! But even in this continuing piece d'resistance of the Canadian National Collection of Insects, there are problems. Things have changed since 1983, there are new genera, synonyms of old genera, and elevated subgenera. And some keys simply don't work very well, or are not trustworthy. This is not true for all the keys, of course. Most of them still work perfectly fine. And even for some of the ones that don't work perfectly, that's just the nature of the game for those groups. I'm looking at you, Tachinidae. It doesn't matter how well a tachinid key is designed, they're the most difficult group of flies and they are going to be difficult until the end of time.

In other cases, however, it's more a matter of updating. Black winged fungus gnats are not the easiest group of flies to identify, but there have been changes since Volume 1 of the Manual was published. What's frustrating is, the Mohrig et al revision is a very nice catalog of all the described North American Sciaridae, with updated names, descriptions, and genitalic illustrations in many cases, but there is no revised genus key. Why? Not THAT much has changed since 1983, it wouldn't be that difficult. Why didn't they include an updated key to the genera in their revision?

This reminds me of another situation.

For about two years now, I have been sitting on this key. It's an updated genus key to the keroplatid fungus gnats of North America, meant to replace a section of the Mycetophilidae in the Manual of Nearctic Diptera. It's even available online, though not exactly pretty. Last week, my adviser said, you know, you should really publish that. Emphatically, he said it. And he's right, I should publish it. But I'm not going to, not now, anyway.

Why? Three reasons:

1. I can't verify it without more research. I've used a combination of several publications, the world checklist, and intuition to build it. But I've looked at very few specimens, and I have no collection to back it up. This was the preliminary work for what was going to be my dissertation, and when I ended up working on tachinid flies instead, well... The Orfeliini is the real problem, with the previous genus Orfelia split up into a large number of what used to be subgenera. Since I don't have a good collection, I don't know if species in the World Catalog are correctly placed. There may even be genera in North America not currently in my key. And I haven't had time to follow up.

2. It needs illustrations. I could quickly and easily format the thing for ZooKeys or the CJAI, but without illustrations it's not going to be easy to use. Especially for all the 'new' Orfeliini genera. I don't have illustrations because I need specimens from all the genera to make them. See item 1.

3. I feel like I'm going to be stepping on someone's toes. I don't think anyone is working on this right now, but I can't be sure. And the key is derived, it's a synthesis; there isn't really any new stuff there, it's a combination of the MND key PLUS Lane 1951 PLUS Vockeroth 1981 PLUS the Manual of Paelearctic Diptera and others. I'm afraid someone is going to accuse me of plagiarism, or of trying to inflate my publication number, or tell me the Manual is good enough as it is, just leave it.

The title alludes to a common saying about identification keys, that they're written by people who don't need them (experts), for people who can't use them (non-experts). Yet they are incredibly useful, even in this day and age when digital HD photographs are a click of a button. Keys are the technology side of our work, they're the tools we create to make our lives easier. Not every specimen is perfect, and not every taxonomic group is nicely defined by a single, specially shared character that no other group has (cf. Tachinidae, again), it's true. Digital identification keys such as Lucid Keys allow much greater flexibility, with multiple starting points, the ability to account for character variability (e.g. lengths), and overall more characters to work with. However, in most cases, a good dichotomous key is much faster to use, in spite of the learning period.

But there seems to be some barriers to publishing keys, especially updates of older works. There's only so many ways I can split up Keroplatidae. Since the parsimonious way is the best way, and since THAT way is the way the Manual is set up, why NOT use the Manual's key as the basis? Maybe my reasons are the same reasons for no updated Sciaridae key in Mohrig et al.

So, some general questions for ya'all:

Is the reworking and synthesizing of old keys into a single, updated key for publication plagiarism?

Is the publication of revisions without dicotomous keys a trend, or is this an isolated case?

How much extra work needs to be put into an update before it becomes worthwhile to publish? Half? One-fourth? The whole shebang?

Do any of you have any keys you're sitting on, not publishing, for the above reasons or others?

Thursday, November 28, 2013

Beating the dead horse Paraphyly.

I know I said I was going to cut back on the ICZNerdery. But this letter by Jaroslav Flegr to Zootaxa this week was too weird to pass up. Morgan Jackson summed it up nicely:

Summary (tl;dr): There is not one shred of anything new here. There's not even anything nomeclature related. The author is using Zootaxa to opine about paraphyletic inclusive classification, that is it, there's nothing else to this "paper" if it could even be called that. (Though, note: the link above only contains the first page and references if you don't have a subscription.)

The title, "Why Drosophila is not Drosophila anymore, why it will be worse and what can be done about it?", suggests this is going to be about the Drosophila melanogaster ICZN case last year. I never wrote a proper post about it, and given the complicated nature of the case I'd prefer not to repeat it here. So check out Kim Van Der Lin's summary in the link if you need a reminder. 

But the title is deceptive. Flegr starts off discussing the case, and he gets one thing wrong immediately. Molecular taxonomic studies have not shown that "the correct name of this species should be Sophophora melanogaster". What they have shown is that Drosophila as it stands now is a paraphyletic taxon. The actual raising of the subgenera to genus level is something that has yet to happen. And when, inevitably, someone revises the genus and raises them, the rest of us can dispute that action. That's right, you heard me correctly. Changing a taxon's rank, changing it's genus, etcetera, are subjective decisions, and unlike the fixation of types are not regulated under the Code. Someone else can come along later and challenge it without getting the Commission involved. D. melanogaster is also not "the fly that eats their fruit". Though they are often called "fruit flies", the common name is "vinegar flies" because they feed on fermenting fluids.

The rest of the "paper" is devoted to supporting a paraphyly friendly classification system, something that seems quite strange to the Cladist majority of taxonomists. Now, mind you, there's nothing in the Code prohibiting paraphyly, but the majority reject it because we've become devoted to a classification system that is descriptive, predictive, and explanatory. We've discovered that when our biological classification is based upon evolutionary descent, and in particular on monophyletic groups (groups that contain a common ancestor and all of it's descendants), it is a powerful general reference system. And when that system includes paraphyletic groups (which contain a common ancestor and only some of it's descendants), it looses predictive and explanatory power.

Flegr moves to his point in a roundabout manner, first starting with an utterly confusing explanation of paraphyly. (Note: Taxonomists are overwhelmingly visual. Reading a long list of possible relationships between Taxon A and Taxon B is about like trying to decipher one of my grandfather's differential equations.) Fer Linneaus sake, use a real life example!  He blames molecular systematics for the multiplication of paraphyletic taxa in recent years, which is a common enough theme in the literature that I don't pay it much attention. All it tells us is that the author is a traditional taxonomist who probably uses physical structures of the organism exclusively.

His statements about "inner and outer similarity" reflect a real problem in systematics, sometimes called the phenotype/genotype conflict. When we infer evolutionary relationships, often times the physical and DNA characters deliver us a differently shaped tree, and we're unable to tell whether one or either of these reflects reality better. But calling it a "conflict" is a misnomer. As one of my committee members recently told me, there is no real conflict between between the morphological and molecular characters. The conflict is in the methodology, and how we analyze the data. Flegr writes "nothing might be possible to guess from a system that would not reflect the inner similarity of the species", as if morphology is doomed to forever represent convergence and DNA is innately neutral to selection. Neither of these are right. 

The deep and real problem that he is reaching for but missing, is that many traditional classifications are based upon obvious physical characters rather than evolutionarily meaningful ones. There are, for example, many characters that place birds as a therapod lineage. But since these are not as obvious as "has feathers" and "is warm blooded", and since this uniqueness is part of a traditional classification, people continue to place them in a separate lineage from other archaeosaurs. Why? Because tradition, because, as Flegr puts it, "secondary school biology teachers are far much more numerous than theoretical taxonomists."

I'll refrain from commenting upon this except to say that allowing high school biology teachers to dictate how we should classify organisms is ridiculous.

Flegr's solution is to allow paraphyletic groups to stand. Of course. What better way to solve a problem than to ignore that it exists? Then you don't have to go through the messy route of educating people. And while we're at it, why don't we just throw out this whole evolution thing? It's so much easier to classify organisms based on obvious characters like, for example, lacking wings. The insect order "Aptera" worked out so well.

There are also some fairly ugly diagrams which are not at all convincing. 

Throughout, Flegr tries to make his case using the prevalence of punctuated equilibrium in major radiations rather than gradual change. Somehow this is evidence for rejecting reciprocal monophyly. I don't see it. There's also the opinion that these phylogenies will make our classification system inherently unstable. To which I reply: They are unstable now. Classifications that are based upon obvious similarities rather than evolutionarily relevant characters will forever be subject to the whims of authority opinions. What Flegr wants is to go back to the days of evolutionary taxonomy, where if Dr. Smith was the expert on so and so group, then whatever he said goes. NOPE NOPE NOPE. 

This is all very much a Dubois-ism, in the spirit of the last paper I wrote about. He concludes,

It is, of course, probable that most of the current theoretical taxonomists, who spent a large part of their active professional life fighting the fuzzy eclectic phylogenetics and taxonomy, would not be very enthusiastic about the recurrent more and more urgent suggestions of rehabilitating the paraphyletic taxa (Hörandl, 2006; Hörandl & Stuessy, 2010; Podani, 2010a; Zander, 2010). The change, fuelled by practical taxonomists who mostly use a ‘wrong’ eclectic taxonomy in their everyday practice anyway, will be probably slow and painful. It is, however, necessary to start the change as soon as possible. Otherwise, we might soon have to say farewell not only to drosophilas but to the whole taxonomic system.
I suspect these authors he cites are all in the same boat, a bunch of "taxonomic reactionaries" who can't cope with their authority being overturned and their traditional taxa being reshaped by evolutionary understanding. They call it "practical taxonomy"; I call it the easy way out. Flegr also shows himself to be a doomsayer by the last line. It's the end of the world as we know it, apparently.

In closing, no, wait. I don't think this mess merits a wrap up. Flegr leaves us one last gift, a tagline. 

"Australopithecus sapiens, possibly Reptilia, Pisces"
  1. Australopithecus does not have priority over Homo
  2. Reptilia is a paraphyletic group.
  3. So is Pisces.

Friday, November 22, 2013

Important kernels lost in the chaff.

There are clear, concise collections of criticism. And then there's this paper. At 94 pages, it's not a short read, so I don't blame you for skimming. It's already received a lot of flack. In short summary, Alain Dubois and 18 other authors published an almost op-ed style article on problems existing in zoological nomenclature, particularly in reference to electronic publication of names and nomenclatural acts. The above links already have eviscerated it.  By that standard, I shouldn't even bother. But wait, what's this?

Given the demands on their time, the ICZN members could probably do without a reprisal of the online versus print naming debate — a debate, remember, that saw the farcical printing to paper of hard copies of online-only papers, which were then handed to libraries to fulfil the exact wording of the code. The Zootaxa authors seem unwilling, or unable, to move on. They have a semantic bee in their bonnet over the code’s requirement that species descriptions must be always “available”. When the online publishers they contacted explained that, no, they did not routinely supply paper versions of the files on the journal’s websites, the authors, rather uncharitably, deemed the information unavailable to them. ---the Nature editorial
Uhhhh.....cue Indigo Montoya. "Availability" does not mean "I can pick it up at the library" under the Code. To be available is to satisfy all criteria within the Code necessary to be considered for validity, priority, and other things. It is a whole lot more than the location of the published work. For example, a nomina novum, or 'new name', is not available unless the type specimen(s) are referenced explicitly, as well as the location where the types are to be deposited. You forgot to do this? Sorry! Your new name might as well have never been put in the literature for all it means to the Code. Refining the articles on availability means that species descriptions have higher standards, which is considered good by anyone who's tried to wade through the old literature.

Given that Nature failed to understand that, a basic and important concept in the Code, I wondered how much more they were flubbing about the article. So I read it. All 94 pages.

What I discovered was, well, a mess. Oodles of footnotes, most of them irrelevant to the paper. CamelCase, really? Symbols in journal names? Philosophizing about supplementary materials? It doesn't matter if I agree with them or not, this is supposed to be a paper about problems with electronic publication of new names. Then there's the intentional emotive, non-academic language. See the footnote on page 29 for an example. And in all things there's this sort of ivory tower dictatorial outlook, as if their opinions are final. Maybe from the authors' point of view they are. The majority of the authors hail from old European natural history institutions. And there's the fact that Dubois cited himself 38 times in the references. 

It's unfortunate that within all this there are some actual relevant criticisms, some of which were not covered in electronic vs. paper debates before the 2012 amendment. For example, some journals mistook the allowance for optical disk deposition (sometimes called the "5-copy rule") to extend to all electronic publications, including PDFs. Which means there are a whole bunch of names between 1999 and 2012 which are not available due to poor reading of the Code. This does not include mixed-model journals like Zootaxa, which publish both an electronic and a printed version with separate identification numbers. In those cases, the printed versions satisfy the Code. The rest, not so much. 

There's also criticisms of pre-publication editions (which make establishing date of publication more difficult), publishing of new names in electronic supporting information (which does not fulfill the criteria of availability, even under the 2012 amendment), and the treatment of online checklists as authoritative. All of these are useful criticisms, as is the main (lost) point of the appendixes, namely, that authors and journals don't understand the changes in the 2012 amendment very well. BioMed Central has responded to the authors' complaints, which is understandable as they took the brunt of the criticism. They reference their editorial policies on describing new taxa, which is available for all to see. They also reference the "5-copy rule", saying they followed the Code. (Note: there is no 5-copy rule in the code anymore. Even if this prior rule could have been interpreted to include deposition not in the form of optical disks, all electronic-only publications before 2012 are considered unavailable.) All of this is irrelevant, as they are still publishing unavailable names even now, after the 2012 amendment. Again, I don't blame them for being upset. The Dubois et al. paper was purposefully inflammatory and should be derided as such.

In summary, there are still problems with electronic publishing of names. But this paper will not be remembered for valid criticisms. Instead, it will be another sign that taxonomy has lost sight of the times. As the Nature editorial pointed out, all the recent ICZN news seems to be bad press. Taxonomists look as if we are a bunch of doryphores, interested more in trivial piddly lawyerisms than solving actual problems. Spend some time on the listservs, for example, or read this paper, it's the same. Without change we'll be irrelevant.