29 May 2009

One Name, One Taxon

One of the primary goals of a nomenclatural code should be to make sure that names refer to one taxon and one taxon only. This principle is mentioned in the ICZN's preamble (emphasis added):
The objects of the Code are to promote stability and universality in the scientific names of animals and to ensure that the name of each taxon is unique and distinct. All its provisions and recommendations are subservient to those ends and none restricts the freedom of taxonomic thought or actions.
This point is reiterated in Article 52:
52.1. Statement of the Principle of Homonymy. When two or more taxa are distinguished from each other they must not be denoted by the same name.
Yet there are numerous cases in zoological nomenclature where this rule is flagrantly ignored. A few:
  • "Echinoidea" is the name of a superfamily containing Echinus (a sea urchin genus), but also the name of a class containing that superfamily.
  • "Ophiuroidea" is the name of a superfamily containing Ophiura (a brittle star genus), but also the name of a class containing that superfamily.
  • "Chelonia" is a genus of turtle, but also used as the name of the order containing all turtles.
  • "Pterodactyloidea" is the name of taxon given various ranks (usually suborder) including most short-tailed pterosaurs, but also the name of a superfamily within that taxon.
This is getting to be an actual problem for me, because parts of Names on Nodes rely on the principle that a name only has one meaning under a given authority. When I create a database entry for urn:isbn:0853010064::Pterodactyloidea, is it for a suborder or a superfamily? ICZN rules actually dictate that the superfamily has precedence, since Family Pterodactylidae Meyer 1830 has precedence over Suborder Pterodactyloidea Plieninger 1901. (The ICZN considers the naming of any taxon whose rank is in the family group as implicitly naming taxa for all ranks of the family group; thus, naming Family Pterodactylidae implicitly names Superfamily Pterodactyloidea, Subfamily Pterodactylinae, Tribe Pterodactylini, and Subtribe Pterodactylina.) People who use "Pterodactyloidea" for a suborder, beware! You are violating the rules of the ICZN! (WhooOOOOoo!!)

The situation with "Echinoidea" is even worse. As near as I can tell, Family Echinidae was named by Gray in 1825 (thus implicitly naming Superfamily Echinoidea), but Class Echinoidea was already named by Leske in 1778. And the ICZN mandates that the superfamily including Echinus must be named "Echinoidea" if the family is named "Echinidae". I'm not sure how this is supposed to play out ... does Echinus simply not get a name for its superfamily? Those poor wee urchins....

(And people wonder why I support an alternative nomenclatural code without mandated suffixes for ranks!)

In the case of Chelonia, people are generally using another name ("Testudines") for the order nowadays, but in other cases I've got a real problem, especially if I hope to automatically pull a lot of this data from other databases.

27 May 2009


Others have said it before me, but I think PLoS ONE and online journals like it represent the future of scientific publishing. Quick turnaround, open access, unlimited space (not just for text, but also images, data files, etc.)—I just don't see how the older forms of journal can possibly persist for long.

Perhaps the most useful feature, though, is sadly underutilized. Imagine this—you're reading a paper and you come across an error, or a questionable inference, or an unclear point. With printed journals, you have the following options:
  1. Write to the editor and/or primary author and hope they have a moment to respond.
  2. Complain to whomever will listen.
  3. Write a frustrated note in the margin and move on.
  4. Fume silently.
But with PLoS ONE, you can accomplish #1–3 all at once. (And #4, if you want.) Simply log in, highlight the text you want to comment on (or click on "Leave a general comment"), and you can leave a publicly-visible note that anyone, authors and editors included, can respond to.

People have been slow to take advantage of this wonderful system, but it's starting to take off, I think. As many are aware, there's been a big media hubbub about a new fossil primate (Darwinius masillae) that may or may not be a stem-haplorhine (i.e., part of the group that gave rise to tarsiers and monkeys, including apes, including humans). I've seen a lot of discussion of it in various venues, and some of that is finally starting to spill over into the paper's comments section. (You may note a couple of comments left by myself.)

One notable outcome of the discussion on Darwinius is the rectification of an incompatibility between PLoS ONE's publication methods and the current requirements of the ICZN. This meant that the new scientific names published in the journal (e.g., "Darwinius", "Darwinius masillae") were nomenclaturally unavailable. Happily, this was quickly resolved, and the remedy was also carried out for the names introduced in some earlier papers.

Other discussions, on such topics as the scoring of characters as "Derived" or "Primitive", are still ongoing.

PLoS ONE also allows readers to rate the articles and leave reviews. (As of this writing, there is one review by Andy Farke, and I think he makes some excellent points.)

Science open to everyone! Go ahead—get involved.

05 May 2009

'Nother Toolshop Animatic: The Head Map

I created a sort of "mashup" of the previous two and added a temporary music track. (The ultimate version will have something different.) Click on the thumbnail (might take a moment to load):

Still clunky, but I'm just fleshing out the ideas at this point. Enjoy!

04 May 2009

March of Man: The Toolshop

My somewhat ambitious web app, March of Man, has not been proving too successful. The idea behind the project is to illustrate human and chimpanzee evolution using hundreds of figures. The web app includes tools for submitting images and generating collages. But there are only a couple dozen images right now. At this rate, the project will be completed by the time I am an old man. Time for a new approach!

I'm going to leave the site up as is, but I am also going to be working on a CG animation. I've made a new area of the website called "The Toolshop" where I'll be posting progress. Here are the first two mockups, using vector animation (click on the image to see the animation):

Human/chimpanzee evolution depicted as streams of bubbling heads.

The ranges of various taxa over time.