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ZooBank Robbery

Rant, Taxonomy, Taxonomy in the News No Responses »

Jun 182016

Since the beginning of the year, I’ve been tracking the newly described animal species that have made the news with their introduction to science, with the intent of understanding what factors make a new species newsworthy. I’m still collecting data and figuring out how to make sense of it all, but in the process I’ve come to realize that a fair number of taxonomists and journals are either unaware of the rules of nomenclature, or perhaps just don’t care.

There are a surprisingly large number of rules that govern how and where new species of animals can be legitimately described, rules that are created and occasionally adapted by the governing body of animal taxonomy, the ICZN. These rules are in place to ensure the language of biodiversity—species, genus, and family names—are consistent and stable worldwide, ensuring that when a scientist in China refers to the genus Micropeza, scientists in Canada, Peru, and South Africa can all understand explicitly what the organism they are referring to is. Without stable names agreed on internationally, we would have a gigantic mess on our hands, and all of biology would grind to a halt.

One of the important tenets of stable names is establishing what name came first, and then using it forever (barring some scenarios in which the oldest name can be suppressed, which we won’t bother going into). This is called the Principle of Priority, and may be the most important (and sometimes, trickiest) rule to follow. Obviously, when trying to address what name was created first, it’s vital to know the exact date that name met all the criteria set forth by the ICZN and was officially coined. Again, there are a lot of rules that stipulate when a name is considered “official”, but one in particular is, for some reason, apparently being ignored more often than the others, and which can cause names to become complicated, quickly.

This rule, introduced in 2012, allows for new species names to be published in digital format (either as an early view version ahead of traditional printing, or entirely digital, like PLoS One for example). Up until this rule was introduced, only names published in journals or other publications that were printed out on paper (in multiple copies) and distributed to a couple of libraries were considered legitimate. But, recognizing that the world of scientific publication is changing (rapidly), the ICZN finally adopted a new rule allowing names to become official in digital publications, but only if the authors take one extra step: register their publications in a new database called ZooBank. This registration process does two things: 1) it allows for papers that have new names introduced in them to be more easily tracked, and 2) the registration process includes a stipulation that the journal intends to archive a non-editable PDF of the paper, so if the internet and all digital media are destroyed, we still (hypothetically) have records of these new names (although I reckon we’ll have bigger issues to deal with than worrying about correct taxonomy in that situation…). Regardless of the intent, these are the new rules, and for any names published in a digital format, the paper must be registered in ZooBank (and state in the paper somewhere that it has been), a process that takes less than 10 minutes to do. Simple enough, right? Apparently not.

In the past 6 months, of the roughly 120 taxonomic papers that have made the news, I’ve found at least 5 that have failed to meet this ZooBank qualification, meaning that any names introduced by the authors aren’t actually real (yet). Five papers out of 120 may not seem like that big a deal, but when you expand that ratio to the roughly 15,000 new animals species described every year, we’re potentially looking at 600 new species that unknowingly remain without an official name!

So what’s the big deal if a few more species remain nameless, there are millions left to be discovered anyways, right? And if the name is being published as an early view in a journal that still releases paper copies, the names will eventually become official once the paper versions are printed and distributed (perhaps weeks or months later). Basically, for scientists that have spent months or years examining specimens and collecting data only to fail to meet this one tiny requirement is akin to a person running a marathon, and then stumbling and falling on the very last step and being disqualified from the race, yet celebrating their “accomplishment” anyways. It may be awkward, or embarrassing, and it should be avoided by all means necessary, but won’t it all get fixed eventually? Well…

Besides the professional embarrassment, there’s a big problem just waiting to happen when names aren’t correctly, and formally, published: someone else scooping the naming rights for your species. Until the name is fully published and all the qualifications met, either by the name being printed out on paper when its assigned issue is published, or alternatively by someone else publishing their own paper that does meet all of the rules, there is no requirement that the name proposed by the original authors actually be used. In fact, nothing is stopping anyone from finding one of these inadequately named species, and turning around a quick paper coining a name of their own for the taxon, establishing priority and ensuring they are recognized for eternity, and not the people who did all the hard work. This type of taxonomic sniping isn’t unheard of, although to my knowledge there have not been any examples of ZooBank robbing, yet.

Is it shady? Definitely. Is it likely to happen? Eventually. Is it avoidable? Absolutely.

So as I’ve stumbled across these named-but-actually-unnamed species by accident, I’ve been sending out cautionary messages on Twitter reminding taxonomists or anyone else in the process of describing a new species about the ZooBank rule, or straight-up condemning repeat-offender journals and advising people not to publish new names in them (looking at you Scientific Reports). Which is what I did again Friday afternoon regarding another new species, published in a prestigious journal that should know better, but which failed the ZooBank test. Unlike previous times however, I linked to the paper, and called out the journal directly, mostly because I hold it in high regard, and also because subtweeting an entire field of science clearly wasn’t working.

To my surprise, within 30 minutes my cell phone was ringing, and the lead author of the paper in question was on the line asking not only what they did wrong, but more surprisingly, that I please delete my tweets calling attention to the issue. The author was aware that the ICZN had recently changed the rules to allow digital publication but didn’t know the specifics, and the journal they submitted to had apparently not published a new species description since the changes came into effect, and so weren’t prepared to comply on the author’s behalf either.

I ended up spending a good deal of time explaining the ZooBank rule to them, and suggesting how they can work with their journal editor to fix it, but I remained uneasy about deleting and retracting my tweets. However, after talking more with the author, and recognizing that they were genuinely afraid of a specific person known for their unscrupulous taxonomic practices learning of their mistake and taking advantage of it, I agreed to take down my tweets, but with the understanding that I would be disclosing the series of events and actions here, albeit with their anonymity intact. Frankly, the taxonomic community has enough challenges facing them, and I’d rather not contribute to those challenges further simply to prove a point at the expense of someone else’s hard work.

So be warned, readers working to document and describe Earth’s biodiversity! Spend some time learning the rules of nomenclature, and ensure that the journals that you submit your science to are equally knowledgeable of what it takes to name a species. And if you’re unsure of a journal’s dedication or experience publishing taxonomic research, take the responsibility for your hard work into your own hands and register your taxa and your papers yourself, and avoid the potential pitfalls of naming species in the digital era. You’ll be glad you did when you see your species spoken of with the name you intended!

BREAKING: Taxonomists are broke & will do what they need to do for funding

Academia, Biology, Rant, Taxonomy 9 Responses »

Jul 032015

This week, Nature published a short Correspondence from Giovanni Strona, a biologist “mainly interested in theoretical ecology”, with a positively shocking revelation: taxonomists are selling the naming rights to new species.

I knew having a fainting couch installed next to my lab bench would pay off one day.

Gender Issues in Taxonomy: more than just Latin

Academia, General Information, Taxonomy 8 Responses »

May 072015

When taxonomists discuss gender, they’re usually debating whether the etymological root of a species name is the same gender as the root of its genus, and whether that species name should end with –i, –a, or perhaps –us. While debating ancient Latin grammar may be a noble, if occasionally dull, pursuit, there’s a more important discussion on gender in taxonomy that we need to be having; why women continue to be underrepresented in our discipline.

I’ve been somewhat aware of the gender disparity in taxonomy for a while—I’ve casually noticed how few women are currently employed in natural history collections or as professors of taxonomy & systematics at universities, and that there are relatively few women attending taxonomic meetings, particularly outside of students and post-doc positions—but the issue burst into my consciousness like a slap to the face recently as the journal ZooKeys celebrated their 500th issue.

As a part of the celebration, ZooKeys created a series of Top 10 posters that they shared on social media, recognizing the editors, reviewers, and authors who have helped the journal become one of the most important venues for zoological taxonomy over the last 7 years. Check them out:

Of the 35 people being recognized for their contributions to publishing & the taxonomic process, in categories that are highly regarded and influential in hiring & promotion decisions, only 1 is a woman. I doubt ZooKeys could have created a starker depiction of gender disparity in taxonomy had they tried.

What’s going on here? How can only 1 woman be included in these lists? Hoping that it was some random fluke, I started looking around for more information on gender diversity in the taxonomic community, and well, it didn’t get better.

First, I looked at the editorial board & section editors for ZooKeys, and found only 1 woman sat on the editorial board, out of 15 members (6.7%), while only 37 of the 265 section editors were women (14%). When I compared this to Zootaxa, the other major publisher of zoological taxonomy, I found the exact same ratio among section editors, 14% (32/225). Systematic Biology? A slightly better 15 for 80 (19%), while Systematic Entomology is 3 for 18 (17%) and Cladistics is only 2 for 20 (10%). Even the small biodiversity journal for which I’m the technical editor only has 2 female editors out of 15 (13%). Meanwhile, the International Commission on Zoological Nomenclature, the governing body that sets the rules for naming animals and adjudicates disputes over names, currently has 23 male commissioners, and only 4 women (15%).

Compare this to ecology, where Timothée Poisot reports 24% of editors for the more than a dozen journals he’s looked at are women, while Cho et al. (2014) found editorial boards in other biological fields to be roughly 22% women in 2013 (up from ~8% in 1990). Clearly 22-24% is a far cry from parity, but it’s still 10% higher than it is in taxonomy.

But is this indicative of the true diversity of taxonomists? It’s hard to say. In 2010, the Canadian Expert Panel on Biodiversity Science surveyed taxonomists in Canada, and reported that 139 of their 432 survey respondents identified as women (30%). Ironically, the panel itself only included 3 women (out of 14; 21%), and only 2 women reviewers (out of 12; 17%), failing to accurately reflect the community it was attempting to assess. Meanwhile, the UK’s House of Lords Science and Technology committee on Taxonomy & Systematics (2008) reported only 143 of 861 UK taxonomists were women (17%), but while there was much discussion over the potential decline in total numbers of taxonomists, there was none regarding gender inequality.

Looking more broadly, 42% of science & engineering PhDs were awarded to women in 2013, and 28% of applicants to the NSF Division of Environmental Biology (the major funding source for ecology, evolutionary biology and taxonomy/systematics in the USA) in 2014 were women, so it’s not unreasonable to assume the professional taxonomic community is at least 25% women, and hopefully much higher. Again, 25% is a long ways from equality, but it still suggests there is a definite misrepresentation of diversity on the editorial committees of taxonomic journals.

So why does it matter if editorial boards and reviewer pools aren’t representative of the community, whether it be in terms of gender or ethnicity (another important discussion the taxonomic community should be having)? Well, for one, keeping taxonomic publishing an Old Boys Club is more likely to result in situations like that which recently occurred at PLoS ONE, with biased, sexist, and misogynistic attitudes influencing not only the publication of research, but by extension, the career advancement (or lack thereof) for taxonomists based solely on their gender. Now, I’m not saying that the editors and reviewers for ZooKeys & Zootaxa are explicitly engaging in biased behaviour, but recent research has shown the implicit biases of academia towards women, particularly in publishing, and there’s no reason to assume taxonomy is immune to these factors.

But there’s also the fact that female early career taxonomists may look at the editorial boards of these journals, or see posters of those being recognized and praised for their contributions, and not see anyone that looks like them in a position of power. Having role models with whom one can identify with is an important influencer, and after 250 years of old white dudes at the helm, it’s unfortunately not difficult to see why gender diversity in taxonomy is where it is.

So where do we go from here? How can we encourage more women to pursue a career in taxonomy and bring their passion for the natural world along with them? Well, for starters, we should be inviting more women to become editors for our journals, but we also need to start talking about gender equality in taxonomy, and our failings therein, more openly. The statistics on women in taxonomy from the Canadian Expert Panel on Biodiversity Science weren’t mentioned at all in the main body of the report, but were instead relegated to the appendices. Worse, the 2010 UK Taxonomy & Systematics Review didn’t include data on gender diversity in taxonomy, instead focusing on funding and age demographics; perhaps illustratively they titled the demographics section “Current Manpower and Trends”.

Ignorance of gender disparity in taxonomy is no longer acceptable; there is no excuse for convening a panel discussion on “The Future of Diptera Taxonomy & Systematics” at an international meeting and only inviting male panelists. As a community, we need to change the way that we go about our work so anyone with an interest in biodiversity feels welcome and able to contribute to our collective knowledge of Earth’s species. Just as we are compelled to debate the etymology of a dead language, we must be equally compelled to create a vibrant taxonomic future based on equality and diversity.

UPDATE (12:02p 05/07/15): Ross Mounce pointed me to a paper that was just published this week that examines the role of women in botanical taxonomy, and they present data that is equally bad to my numbers above. Of the nearly 625,000 plant species described over the last 260 years, a paltry 2.8% were described by women. Additionally, only 12% of authors in botanical taxonomic papers were women. Read the paper in its entirety in the journal Taxon.

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Cho A.H., Carrie E. Schuman, Jennifer M. Adler, Oscar Gonzalez, Sarah J. Graves, Jana R. Huebner, D. Blaine Marchant, Sami W. Rifai, Irina Skinner & Emilio M. Bruna & (2014). Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management, PeerJ, 2 e542. DOI: http://dx.doi.org/10.7717/peerj.542

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For the biodiversity data scientists reading this, a challenge: what proportion of authors in taxonomic papers are women, are they more likely to be first author, last author, or somewhere in the middle, and what proportion of taxa have been described by women? I think these statistics should be relatively easy to figure out, especially with services like BioStor & BioNames, and will help us better understand gender diversity in taxonomy, both historically and as we move towards the future. And perhaps consider publishing your results in the Biodiversity Data Journal, which has editorial gender issues of its own (editorial board: 1/14 (7%); section editors: 28/161 (17%)).

A Blank Page

Life as a Grad Student, Thumb Twiddling 8 Responses »

Mar 302014

The blank page, the biggest obstacle to my success.

I’ve been thinking about this post for 4 years. I’ve reworked what I want to say countless times on my walk to and from the lab and considered ways to tie it all together while laying in bed staring at the ceiling, but, until last week, I didn’t know how, or even when, it would begin.

I’ve put off writing about blank pages and my writing struggles because it so often begins with me staring at, and subsequently backing away from, a blank page. Did I mention I have a problem writing when faced with a blank page?

By late 2010 I had a full molecular DNA dataset prepared and analysed for my Master’s that showed some interesting relationships among the flies I study, and I proceeded to write up the results for my thesis. I moved on to the other major chapter of my thesis, and then defended my work. The whole thing was well received by my committee, and I was granted my degree in 2011 with the expectation that I’d make a few relatively minor changes and then submit the chapters for formal peer-review.

Well, after the final few months of pushing to get my thesis ready to defend, I needed to decompress and had no desire to look at my work for awhile. I figured after a few weeks of doing something — anything — else, I’d be ready to come back and reanalyse the data, rewrite the paper and submit my work to an appropriate journal, and then never have to look at it again. Instead, I got busy working on other projects, writing a book, teaching, and then eventually starting my PhD, all the while having this paper hanging over my head, like a rusty guillotine just waiting to fall.

It wasn’t long until every word I wrote for the blog, for grant applications, or even emails elicited an increasingly larger pang of guilt that those words should be going towards that paper, to the point that nearly every aspect of my life was tainted by anxiety over it.

For nearly 4 years I let it slide while busying myself with other projects and tasks, telling myself that next week will be the week that I look at it again, until this fall when (with a not-so-subtle nudge from my PhD committee) I forced myself to get it done, or perhaps die trying. After all new analyses, totally redrawn figures, and about a dozen written drafts spanning several months, I finally submitted the paper two weeks ago. The feeling of relief when I finally pressed that submit button came immediately, and I finally realized that I hadn’t been devoting my full attention to any of my other projects or responsibilities.

So why bring all this up now when the paper hasn’t even gone out for review, and will undoubtedly require more work post-review before I can finally be done with it? Because I need to get over my hesitancy to put my thoughts on paper (or whatever this digital equivalent of paper should be called), and I suspect I’m not the only one who faces these obstacles.

My qualifying exams are coming up, which means several weeks of intense studying followed by days of writing compelling papers in a set amount of time, on demand. I’ve always approached this blog as a tool for self-improvement, so I plan to continue using it to force myself to write more frequently, to get past my fear of that blank page.

And for anyone out there currently in the midst of graduate work or projects that require writing, don’t let that blank page stand in your way: all it takes is one word scribbled down to defeat it.

“I got it there then” – Reid Moran, 1962

Biology, Fun Stuff, Natural History, Taxonomy 5 Responses »

Jul 102013

In what will probably be the only blog post I ever write about plant taxonomy, I bring you one of the greatest natural history papers ever published:

Cneoridium dumosum (Nuttall) Hooker F. Collected March 26, 1960, at an Elevation of about 1450 Meters on Cerro Quemazón, 15 Miles South of Bahía de Los Angeles, Baja California, México, Apparently for a Southeastward Range Extension of Some 140 Miles

R. Moran, 1962 (Madroño, 16)

Yes, that’s the full title of the paper. The introduction/methods/results/discussion reads as follows:

I got it there then (8068).

which is then followed by almost a full page of hilariously detailed acknowledgements thanking everyone who had a hand in this rigorous scientific study. You can read the full work in all it’s glory here.

In case you were curious, Cneoridium dumosum (or bushrue as it’s commonly known) is a species of flowering citrus shrub known from southern California and, thanks to Dr. Moran’s dedication to publishing his findings, northern Mexico.

Cneodidium dumosum flowers, which in this humble entomologists opinion, are fully deserving of such an awesome place in the history of the taxonomic literature. Photo by Stickpen, public domain.

I can’t help but wonder how a journal would react should you try something like this today; would they have the good nature to publish it, or is this an auto-reject-in-waiting?

Thanks to Chris MacQuarrie for his photographic memory archiving the entire discussion section of this paper and bringing it to my attention, and Rafael Maia for helping to get me a copy of the full text. My sincerest apologies to Rafael’s lab mates for his subsequent & uncontrollable laughter.

UPDATE (July 12, 2013): After George Sims inquired about the “(8068)” in the comments below, I turned to Twitter to crowd source the answer, and sure enough, got an answer! Tyler Smith (@sedgeboy), a botanist at Agriculture & Agri-Food Canada in Ottawa, hypothesized the number was the author’s collection number for the specimen, and then proved his point by finding specimen #8071 in the Missouri Botanical Garden’s database, which was collected on the same day and at the same location! Why Dr. Moran didn’t include this with the rest of the collection data in the title of the note is a bit odd, but as nothing else about this note is “normal”, I suppose anything goes!

Also, David Shorthouse (@dpsSpiders) found Dr. Moran’s obituary, which provides an interesting overview of the life of a legendary naturalist and field biologist.

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Moran R. (1962). Cneoridium dumosum (Nuttall) Hooker F. Collected March 26, 1960, at an Elevation of about 1450 Meters on Cerro Quemazón, 15 Miles South of Bahía de Los Angeles, Baja California, México, Apparently for a Southeastward Range Extension of Some 140 Miles, Madroño, 16 272-272.