Published on 17 January 2025

This week, my first paper on zoological nomenclature was published. It’s not my first zoology paper – I wrote some horrendous papers on laryngeal air sacs in Homo during my second masters. But it’s the first paper I’ve published talking about the names of living things, and the first new paper I’ve had in the literature for a couple of years.

You can read it here: Corrections for grammatical agreement in Ophiodermatidae. In short - I changed the names of some brittle stars, a relative of the star fish, so that the species name agreed with the genus name, as is necessary under the International Code of Zoological Nomenclature (ICZN, or the Code), which outlines how scientific names should look.

So, Ophiopsammus maculata should be Ophiopsammus maculatus, for instance.

This is kind of a weird thing to do. For one, it’s odd because it’s difficult to understand the Code. The ICZN is used by everyone across the world who uses a Latin name for an animal (except if you’re talking about butterflies, because lepidopterists are intense anarchists and more power to them). If you knew that humans are called Homo sapiens, and if you understood my first paragraph, you’ve used names that are described according to the Code. But this Code is really long, really technical, and also confusing, contradictory, and obscure.

It does say in Article 31 that species names need to agree with genus names, but how to do that well takes some knowledge of Latin or Greek, which most biologists don’t have. So, people mess up sometimes. And those mess ups, according to the Code itself, should be corrected.

Most people don’t bother correcting names, or, if they do, they do so as curators or taxonomic editors working on large projects. It is very rare to find papers on grammatical agreement coming from members of the public, and it’s a bit unclear if taxonomists even have to agree with them or implement any changes made in those papers. That makes sense - the main people editing Wikipedia are the few people who really understand Wikipedia, for instance, and big changes are normally done only by people who have understood how it works for a while. That’s how it is in any community.

But that doesn’t stop other people from getting involved. So, when I saw a brittle star that I found in a tide pool had a Latin name that didn’t make sense to me, I wrote a paper describing how the name should be changed to make sense. That is what the paper I wrote does.

Since publishing it, I’ve had a discussion a taxonomist about why I bothered making these unnecessary changes to species names. I’ve written a response, which I wanted to share more widely for those who are interested in why I think this work matters.

Here it is.

The Code is a monumental work because of its global relevance. Any educated person would recognize a scientific name. I think that is fascinating and awesome. As someone who works on protocols and with communities building digital infrastructure for society as part of my work in the open source ecosystem, the scope and breadth of the Code is really interesting to me from an anthropological perspective.

It is also deeply flawed. There are a lot of issues with it. The gender agreement clauses are confusing and occasionally contradictory. You can’t name a patronym after a non-binary person. The code is Eurocentric to the point of being explicitly colonialist. And the processes that the ICZN uses for updating it are byzantine, vague, and exclusionary (for instance - who is talking about abandoning agreement? How is the public involved with that?). Zoobank doesn’t currently fulfill its mandate. And species names don’t work well for classifying life, as is increasingly apparent for things like viruses. None of these controversies are new.

However, the Code does exist, and its authority is basically unquestioned. And the code does include grammatical agreement as standing articles within it. You’re right that Latin isn’t commonly known anymore (and much more so for Greek). So this creates a lot of confusion for people naming things. I think part of this confusion stems from the process where you don’t need a publication to use the correct name - meaning that Ophoipsammus maculata, O. maculatus, O. maculatos, and O. maculatum could all be at some point used by people who are trying to figure it out. Having a publication about changes in agreement makes it easy for people to point to that publication to say, “Here is the reasoning behind a change.” I think that that is helpful, because it clears up some of the confusion around names. O. maculatus was used in at least one paper that I found last night, but not by WoRMS - which means that confusion already exists in the literature for these names, and which could hamper search efforts by researchers using the internet. I don’t think just editing it is as useful as talking about why it is edited. And a species-by-species account, when people work on them, often doesn’t include these notes or overlooks broad changes that should be made.

“Necessary” is a word I would use for describing these changes, because I think that fixing errata should leave a papertrail, just like a Wikipedia edit should have a sentence describing the edit. And if we’re all going to use a Code, we should use it as it is currently written. I don’t mind the lepidopterists going their own way - at least they’re clear about it. A papertrail really helps with charismatic zootaxa like birds or turtles - the screeds written on why a name is what it is are helpful when a lot of people are invested in the correct spelling of a word.

The overwhelming response I’ve gotten from zoologists already in the establishment is “don’t bother”. I disagree with that injunction. I want to do what I can to be part of the conversation. It’s very rare for me to find a field where I can combine my work on protocols, open source, and open science with my Linguistics background - I have a masters (hons) in Linguistics and an MSc in Computational linguistics - and with my classics background - I teach Latin at the high school level, and did Greek for a few years in university. I applied to the ICZN to be on the commission this year, and wasn’t put on the slate, but have spent a lot of time talking to some of the commissioners about this sort of work, and want to continue doing that.

I wrote this paper on O. maculata because I found one in a tidepool and thought, “Huh, that name doesn’t make sense”, and just like putting it on iNaturalist (https://www.inaturalist.org/observations/251421946), or creating the Wikipedia page (https://en.wikipedia.org/wiki/Ophiopsammus_maculata), changing the name is something I can do as a citizen scientist just interested in the world and how science works. It wasn’t a concerted, intentional effort to start here - I’ve been writing a few of these papers on other taxa, and am working on a much more thorough work on birds.

This paper on brittle stars is really small in scope, because I am still learning the system and how it works. The intent is never to shame other people for making mistakes in Latin, but rather to find out how and why the Code fails to make it easy for those people to do their work. I could make that clearer in my papers.

Don’t expect a lot of gratitude. Some may be happy, others will just wonder, who has time to spend on such housekeeping activities.

I don’t expect a lot of gratitude, but my hope is that people won’t take these things personally, because they’re not personal attacks. It’s the Code that is failing people, not the other way around. As for how people want me to spend my time – who cares? That’s not up to them. And hey, this work is fun!

Thanks for helping me understand that [how this process works]. The Code has a lot of unspoken rules around it (one could be “don’t change species names for grammatical agreement and expect to be thanked”).

There’s another argument for why I bothered that I didn’t get into in my response: science is about communication. Journals and books are just ways that people talk to each other, building up the world through words, just as blogs and social media posts also determine how we understand what each other are doing and how we should orientate ourselves.

Viewed in that light, the statement the taxonomist made that “this work is unnecessary” is really interesting to me. I’ve had several people tell me that working in this field is a waste of time, that I should “go grey elsewhere”, and that it is a rabbit hole that people fall down.

And a few people, mostly friends, have told me the opposite - that naming things is important, that I should follow my passion and curiosity, and that they think that this problem is the most Richard-shaped problem they’ve seen.

There is no God. There is no ultimate arbiter of the necessary. How we talk and what we do with our time is a personal prerogative. One could argue, probably correctly, that I am being ineffectual with these papers, in the sense that some people see it as bureaucratic silliness and they don’t think the spelling of maculata or maculatus is important, and the people who determine names in the major taxonomies could just ignore me.

But I think names do matter, because they determine how we understand the world. And the protocol behind naming matters, because it influences how people feel about names - whether they are easy to understand, or not, and whether science as a process is open to the laity, or not. Changing names for grammatical agreement and talking about that process is one small edit on Wikipedia, one piece of rubbish picked up off of an endless beach. And each small act adds up.

I once sat down with a friend of mine, a mother of four and an excellent birder. While we talked in her backyard, a Common Grackle walked by. I interrupted the conversation to say “Quisculus quiscula.” She asked me what I said, and I said, “That’s the Latin name.”

She turned towards me: “We don’t use Latin here.” I asked her why, and she mentioned something about exclusionary language. How I wish I had remembered what she said verbatim!

“Sure,” I responded, “but doesn’t it sound nice? It’s a fun word to say! Quisculus quiscula.” She paused for a second, and then tried out the sounds. Yes, she agreed, they were fun. Then her kid said it, too. I was overjoyed.

I think about that interaction a lot. What is it that turns something that is difficult, pretentious, unattainable, or obscure into a joy? And who decides how we approach the world?

The answer to the second question is, of course, that we do. Even if the work is seen as silly or useless or annoying by some, I don’t see it that way. And each small publication is me learning more about a system, so that I can go on to see if I can influence it in other ways - perhaps through eventually changing the code, or by pointing out issues that I notice that others who don’t have my background don’t. That’s all science, and it’s all part of what makes Homo sapiens into sapiens.

If you’re interesting in this stuff, I’d be really happy to hear from you. I’m a member of a community of taxonomists who want a decolonialised, trans-friendly, non-exclusionary, and non-Eurocentric world. Fixing the Code is part of that work.

Hit me up if you’d be keen on joining our discussions.

Published on 18 December 2024

I want to share stuff, and I don’t think I can easily, because of how publishing works.

I am currently going through a large list of scientific names for birds, looking for issues where grammatical agreement needs correction. In short, the ICZN has a Code which moderates how all scientific names - the Latin ones, like Passer domesticus or Homo sapiens, are properly formed and used. Part of this list concerns species names, which have to agree in gender with their genus (domesticus, masculine, must agree with Passer, masculine). People often get this wrong, because Latin and Greek are hard, and because the Code itself isn’t always clear.

Right now, I am going through a host of names from South America. As I am finding names which are to be corrected, I am marking them out, and writing about them for a future article to publish somewhere, with peer-review and in, hopefully, a reputable journal like Zootaxa. This work is laborious, interesting, and delightful.

A problem I’ve been having with the work is that, besides my long-suffering partner and roommates, there’s few people I can talk to about this work. If I post about a species name online, I’ll need to cite myself when I write the journal article. If I post about a species name on Codex Mutabilis, my journal for publishing name corrections validly according to the ICZN, then I can’t include those corrections in a future publication - they’re already done. But all of the interesting ones belong in this category. I could post about the other ones, but they’re not as fun.

Take, for example, Crypturellus obsoletus, the Brown Tinamou. Look at that bird. It looks great.

But its name is confusing. obsoletus is clearly a masculine Latin adjective - note the -us ending. That word is only an adjective, in both Classical and Medieval Latin, so it could and should be changed to match the gender of Crypturellus, which has been done here. So, the gender of Crypturellus has to be masculine.

But how can we know that? Well, it must come from Crypt+urus, probably. That means something like “Secret tail” in Greek. That’s what the etymological dictionary that Birds of the World uses says, too: “Gr. κρυπτος kruptos hidden; ουρα oura tail.” This has been transliterated well according to best practices - the kappa becomes a c, the upsilon a y, and so forth. But how does ουρα become urellus?

Birds of the World notes it came from Crypturus Illiger 1811. That means that Illiger was a scientist who published making that name in 1811. The problem here is that the ICZN Code doesn’t allow something that late to be Latin - Latin is only from the Classical and Medieval period, according to their Code’s glossary. So, it can’t be from that.

Here is the original description of Crypturellus by Brabourne & Chubb, 1914, which you can read here on archive.org.

Notice there is nothing about etymology in there, except mentioning Crypturus.

I suspect that most people reading this would point out that urus is the last word, and that urellus is just the diminutive, so that’s fine, that looks masculine. But technically, urus is not a well-formed word in Latin or Greek for “tail” - it’s a Latinized form of ουρα, which should have been transliterated as oura or more commonly ura. And even then, -ellus is a Latin suffix, not a Greek one. It could only apply if urus was Latin.

The Code doesn’t care about the etymology or whether a word is a mixture of Latin or Greek. But it does care about whether a scientific name ends in a Latin or Greek word or not. So, is urellus a word? Or, perhaps, some other form - Crypturellus, Rypturellus, Ypturellus, Pturellus, Turellus, Urellus, Rellus, Ellus, Llus, Lus, or Us?

Technically, both Turellus and Lus are words - both masculine nouns. But they are both also sort of not useful words - because they clearly weren’t intended. Another one is urus, which is a masculine noun for “aurochs” (an extinct bovine animal), and urellus would be a valid word for “the little aurochs”, although one wouldn’t find it in the dictionary. It would also be masculine.

None of these three words are great. The last one is the best, because at least Crypt is a word, although, again, technically, the Code doesn’t have anything written about making sensical divisions. The Code also doesn’t talk about what to do if a word ends in multiple words at different points - how does one choose?

The clearest thing to do here is actually to use none of these words at all. Instead, either treat it as ουρα transliterated into urus, with an added suffix, which is masculine. The code actually talks about this a bit - “a Greek word with a change of ending”, it says in Article 30. Or, treat the whole thing as a non-Latin or Greek word, as Cyrpturus as the name was intended isn’t a Latin word according to the Code, because 1811 is after 1500.

I favor the second one, because it makes the most sense to me. The former doesn’t because I don’t know how to scope where the ending was changed. What’s stopping me from calling “Crypturus” the word for “Gaia”, with a very changed ending? Nothing except common sense. But common sense differs across people, and can’t be measured, and isn’t codified in the code anyway. The second one doesn’t depend on that as much. Crypturellus is simply not a Latin or a Greek word, under any definitions of those words.

Ok, so Crypturellus is masculine according to the Code, because it is not from Greek or Latin and it looks like a Latin masculine word. What does that mean for the other species names? Nothing. Everyone has already been assuming that Crypturellus is masculine. There are very few ways it could be anything else – technically, it could have been if it wasn’t based off of Latin or Greek, and if the original authors made it available (used it for the first time) with an adjectival species-group name that was feminine. They use it at first with a species name ending in rostris, which makes it a noun, and the other name they use with it, tataupa, is also a non-Latin and non-Greek noun, as they explicitly state it came from Güaraní. So, again, it is masculine. Everyone has been assuming correctly. Nothing needs to be changed.

On to the next name.

This is the work which I am doing in between other work, because I like it. But all of the sleuthing above does nothing and goes nowhere, because it’s not worth publishing, and it’s not worth posting about. It’s interesting to me, though, but that’s all. It also takes far more time to write up than to actually do. The stuff that is more interesting comes when the conclusions I come up with mean that people have been reading the Code wrong. And I’d like to share those, but I’m not sure how to, until I finally publish the thing.

If anyone has ideas on how to publish or share that without sniping myself, let me know.

Published on 11 December 2024

In my last post, I talked about applying for an ISSN. In short, I wanted to get one because the International Commission of Zoological Nomenclature has a code, which mandates how scientific names are made - and names are only made valid according to that code if published in particular types of publications. Getting an ISSN would be one of the ways to make an independent website like this into a valid place of publication.

Unfortunately, I heard back fairly swiftly from the National Library of New Zealand: No, I can’t have an ISSN for burntfen.com. The reason is that personal blogs are not suitable for ISSNs, according to the ISSN’s own website. This is interesting, as Jessamyn West followed this blog and got one for her website. But I was stymied for a few seconds - what can I do, instead? How do I make a blog that would be considered valid?

An day later, and Codex Mutabilis was live. A day later, the NZ library gave it an ISSN! Excellent.

Codex Mutabilis is a Jekyll blog running on GitHub Pages, with a new domain and an about page that makes clear that it isn’t a personal website, and is made exclusively for publishing scientific names for the ICZN. Because it’s a GitHub Pages website, there’s even an easy process for people to submit new names if they wanted, by making a pull request. After talking to Jessamyn on Mastodon for a bit, she agreed to join the editorial board (as long as there was no work involved, which is fair!). So, we now have an independent, new, microjournal.

This is pretty cool!

I’ve made a few posts already. I searched for a few minutes after setting up the page, and quickly found some issues in the taxonomy on WoRMS. One of these I have now registered on Zoobank - which took a few minutes, as I also had to register it on Zenodo to get a DOI. Both of those tasks are somewhat mundane and arduous, and I am going to think on ways to improve them.

For now, though, Prunum boreale is now Prunum borealis. As far as I can tell, this was a valid nomenclatural act, published on the site. The issue was minor - an adjective is also a noun in Medieval Latin, and so shouldn’t have been changed when it was. Publishing corrections like this is normal, although they’re normally a footnote to wider papers.

There are a few questions that jump out to me from this work. First, doesn’t the work need to be peer-reviewed? I don’t think so. The ICZN doesn’t specify that, and you don’t need to have work be peer-reviewed to be valid in a journal. I can’t put it on my CV as a peer-reviewed publication, but “Prunum boreale (A. E. Verrill, 1884) is changed to P. borealis” is, for all intents and purposes, published.

Secondly, why? What’s the point?

My answer to that is mixed. First, I wanted to do this because I wanted to see if I could. Curiosity is as good a reason for doing something as anything else.

But the second reason is a bit more complicated.

The ICZN Code is how we know what scientific names are formed correctly. If you’ve ever heard the term Homo sapiens, or Passer domesticus, you know what scientific names are. You probably wouldn’t expect to see a scientific name formed like You are a really good dog, aren’t you?. It doesn’t even make sense to think of that as a scientific name. The Code is what prevents that from happening.

However, there are a lot of issues in the taxonomic code. It is difficult to understand, confusing, and at times, contradictory. Most names are fine - but there are several bugbears that are crawling out from under the rug. For instance, you can’t name an animal after a person of non-binary gender. Or, a species name that is spelled wrong needs to stay spelled wrong, but if a species name is spelled the same as a Latin adjective by accident, it needs to be changed if the gender doesn’t match the genus. Or, genders of non-European languages aren’t even considered in the code unless a scientist explicitly notes them, but that isn’t the case for German or French. Or, any name ending in -ops is masculine, forever (unless the Code ruled in an opinion that it isn’t). The list of strange rules goes on.

Consistently, I’ve come across statements in the literature or talking to others that some of these issues shouldn’t be addressed immediately, because to do so would upset hundreds or thousands of names. That makes sense to me - but it also means that people get confused. Names get changed when they shouldn’t. And then have to be changed again. There’s a lot of time wasted on understanding Latin and Ancient Greek rules, when those languages have been functionally dead for a while now.

Understanding these concerns and issues takes a good amount of time, and then trying to fix them takes more. This is the kind of work that takes a lifetime to do well. Especially when you have to go through the peer-review process, and explain how the code works to reviewers, or why a word is or isn’t Latin. All of that work takes time and effort that could be better spent somewhere else, if the code was different.

Or if publishing was different.

That’s the point of Codex Mutabilis. It’s a fast, lightweight way to change lots of names. I imagine it is also horrifying to some academics - it breaks the social contract we’ve agreed on for how names work.

I see this from a different angle. Publishing on Codex Mutabilis isn’t any more or less worse than publishing on Zootaxa or in Nature. It’s exactly how the Code currently works. I’m not publishing things that aren’t valid or in a way that the Code doesn’t allow - I’m using the requirements listed by the Code itself. If the Code is broken, maybe the Code should be fixed itself?

If the Code is more like guidelines, than it isn’t a code. If the social contract doesn’t work, then there ought to be another way to do things.

At the same time as I am working on Codex Mutabilis, I am also working on several articles about nomenclature that address issues in the more regular way. I’ve gone through the entirety of the BirdsNZ list of birds in Aotearoa New Zealand for errors according to the code, and found several. I’m halfway through the list of British birds published by the British Ornithological Union, and I’ve found more. I’m working on an article about these, and am hoping to submit it to an actual journal soon. But in the meantime, small things can go on this new website.

I’d be happy to talk about this with anyone, and more than happy to learn that Codex Mutabilis isn’t actually valid. Let me know! You can email richard@codexmutabilis.com, of course. We’re also looking for editors, if you’re interested in being involved with peer review.

Published on 03 December 2024

Today I’ve applied for this blog to have an ISSN, so that I can fix issues in Latin names for animals more easily.

The International Code of Zoological Nomenclature is the standard by which scientists in zoology know how to properly name species using the Linnaean classification system. It’s the reason that humans are known as Homo sapiens and not Homo the people who walk upright who think they know everything, and why Black-capped Chickadees are called Poecile atricapillus and not Those really cute birds formally. When you see Latin names in books, those books have been well formed according to the Code.

The code is long, and has a lot of bits about how to make Latin names look good. It also has sections specifically about grammatical gender agreement. This determines why the Duck-billed Platypus is Ornithorhynchus anatinus and not Ornithorhynchus anatina (not that the ending is different). These rules are normally followed very closely, but they have some issues. At times, they are conflicting. They privilege Latin and Greek over other languages, and European languages over the rest of the world. They allow options for naming species after people only if they are male or female, and not nonbinary. The code needs some work.

Sometimes, changes are necessary. This only happens when gender agreement was messed up, or if a different name has priority in the literature, or if there was a spelling error or something. In order to make these changes, one normally needs to go through the scientific review process, or to publish a name change in a reputable journal or book. For instance, a PhD thesis would be an acceptable place to publish a name change, if one ran across one in the work, just as it would be an acceptable place to publish a new species. This is what keeps personal letters from being places to define species; you need to announce them somewhere where scientists would read about it.

This is what I have been doing most recently. Going through the scientific literature, I have occasionally noticed that some of the Latin names don’t match the respective genders of their genus. An example is Ophiopsammus maculata; psammus comes from the Greek ψαμμος, which can be masculine or feminine, and it was translated with a changed ending, -us. Under the ICZN, that means it should be considered masculine. So, maculata should be maculatus.

I pointed this out by writing a short note - a two page journal article that goes over all of the species in Ophiodermatidae and suggests changes for the species that need to be adjusted. I submitted this to Zootaxa, and it was accepted, and should be published fairly soon.

This is a long process - it had to go through peer-review, editorial review, and then be published. I started to wonder if it was necessary; is there another way that I could publish these changes? How reputable does a venue need to be to make nomenclatural acts formal?

It turns out that “reputable” is pretty clearly defined in the ICZN code, in Article 8. I’ve listed these points below. As you read them, ask yourself: What is stopping a web blog from being a place to publish things?

8.1. Criteria to be met

A work must satisfy the following criteria:

8.1.1. it must be issued for the purpose of providing a public and permanent scientific record,

8.1.2. it must be obtainable, when first issued, free of charge or by purchase, and

8.1.3. it must have been produced in an edition containing simultaneously obtainable copies by a method that assures

8.1.3.1. numerous identical and durable copies (see Article 8.4), or

8.1.3.2. widely accessible electronic copies with fixed content and layout.

And then, in 8.5:

8.5. Works issued and distributed electronically

To be considered published, a work issued and distributed electronically must

8.5.1. have been issued after 2011,

8.5.2. state the date of publication in the work itself, and

8.5.3. be registered in the Official Register of Zoological Nomenclature (ZooBank) (see Article 78.2.4) and contain evidence in the work itself that such registration has occurred.

8.5.3.1. The entry in the Official Register of Zoological Nomenclature must give the name and Internet address of an organization other than the publisher that is intended to permanently archive the work in a manner that preserves the content and layout, and is capable of doing so. This information is not required to appear in the work itself.

8.5.3.2. **The entry in the Official Register of Zoological Nomenclature must give an ISBN for the work or an ISSN for the journal containing the work. The number is not required to appear in the work itself.**

8.5.3.3. An error in stating the evidence of registration does not make a work unavailable, provided that the work can be unambiguously associated with a record created in the Official Register of Zoological Nomenclature before the work was published.

I have bolded 8.5.3.2. Why? Because if you read the code clearly, there’s nothing that eliminates this blog from being a place to publish nomenclatural acts - except for this point. This website doesn’t have an ISSN - why would it? Those are for publishers, and people who want their work to be archived somewhere. But those publishers got their ISSNs assigned to them from somewhere, though. In the case of Aotearoa New Zealand, that place is the National Library, where there is a handy form for requesting them.

I have now sent in an application on that form.

I don’t need to be able to perform nomenclatural acts on this website. I could go with the process I have currently been doing, using journals and the review process. But I am curious about this workflow. It would help - for instance, right now I’ve had a paper stalled for four months by an unresponsive editor. With this, I could publish immediately.

The ICZN’s stated goal is to preserve stability in taxonomy. That is incredibly clear. But the ICZN also mandates how names should be made. Publishing is an arduous process. But it doesn’t have to be.

We’ll see if this process works. After getting an ISSN, I need to submit the blog to the ICZN itself as a publishing venue. Updates as they happen.

Published on 31 October 2024

As of last night at the AGM, I am now a new Committee Member for PythonNZ. This is the local community group for the Python language and ecosystem, here in Aotearoa New Zealand. We hold meetups and host an annual event called KiwiPycon. While I don’t use Python in everything, I do use it almost every day I am on a computer, and it is great to be able to support and be a member of a local tech community.

I gave a talk at the first KiwiPycon I attended, in 2024, on iNaturalist and eBird. You can watch it here.