02 May 2012

The PhyloCode Will Not Be Amended

At least for now.

In a 10-1 decision, the Committee on Phylogenetic Nomenclature voted to reject the wholesale adoption of a proposal to amend the PhyloCode that would have greatly changed how it handles species and species names. However, the CPN has decided to discuss the possibility of using some ideas in the proposal.

As I discussed earlier, I'm open to following the proposal in removing the term "species" from some places. E.g.:
2.1In this code, a clade is an ancestor (an organism, population, or species) and all of its descendants.
I see no reason this couldn't just be:
2.1In this code, a clade is an ancestor (an organism or population) and all of its descendants.
...especially since species are almost universally considered a type of population.

In fact, I'd prefer this:
2.1In this code, a clade is a taxonomic unit and all of its descendants.
...or ideally:
2.1In this code, a clade is a cladogen united with all of its descendants. A cladogen is a taxonomic unit, or the union of multiple taxonomic units that all share descendants and are not ancestral to each other.
...but that's a larger change that would have little, if any, practical impact, and hence would be better discussed at a later date, well after the code is up and running.

Anyway, I'd like to see what readers of this blog think about the matter. Comment away!


  1. I hate to be negative again (after last time!) but ...

    Please, no. If the PhyloCode is ever going to be more than a little special-interest pursuit that a few of us go off and do in private between consenting adults, then it needs to be comprehensible and approachable to the other 99% of taxonomists. They know what they and we mean by "species". They have no idea what you're talking about when you say "cladogen", and it doesn't help to say "a cladogen is a taxonomic unit, or the union of multiple taxonomic units that all share descendants and are not ancestral to each other". The best case is that will say, "Oh, so sort of like a species then", and mentally substitute "species" wherever it occurs.

    Please. Come on. As a long-time programmer, you must be familiar with Henry Spencer's classic Ten Commandments for C Programmers. I draw your attention to commandment 8, which applies as follows: "Thou shalt make thy nomenclatural code clear to thy fellow man by using the standard term 'species', even if thou likest it not, for thy creativity is better used in solving problems than in creating beautiful new impediments to understanding".

    1. What part of "well after the code is up and running" are you missing?

    2. Well, then the question becomes why are we even discussing it now? All it can achieve is to make PhyloCode skeptics more cautious and PhyloCode opponents more strident.

    3. Oh, okay, let me clear it up.

      We should discuss this change now:

      "2.1. In this code, a clade is an ancestor (an organism or population) and all of its descendants."

      And the "cladogen" and "taxonomic unit" stuff at a much later date.

    4. One of the possible problems with the current draft is that it locks us in to a variant of the Phylogenetic Species Concept: http://www.ohio.edu/phylocode/glossary.html#term-species

      Getting rid of any dependence on any species concepts would be a good move for right now, in my opinion. Such changes would not have to be excessive.

    5. Wait, Mike (Taylor): How can I not apply your aphorism to "genus"? Or any historical entity for which a functional use remains persistent? Applying Spencer's "commandment," the form follows convenience of not making people learn wholly new systems of language and nomenclature. But by the same token, drastic leaps in language evolution don't occur. Imagine if Newton were confronted with this and never developed Calc!

      (I do agree that not throwing terms around that seem alien is more useful. Sometimes it is necessary to point this out by example. But, there is also the need to abandon what doesn't work, and the baggage the Linnaean System applies to systematic biological nomenclature makes it very difficult to bridge actual evolution from the rung-based system Linnaeus had when he developed the system -- and thus how it is used today.)

    6. Good point, Jaime.

      (The original rule is more about orthographic style than vocabulary, anyway.)

  2. I just spoke with someone who participated in that vote and even he (name will not be supplied publicly) has become pessimistic about the Code ever being enacted.

    Honestly, I'm more or less over it. The PhyloCode is imperfect but much better than the ICZN except for one key issue: The ICZN is published. Until the PhyloCode shows some movement to close this make-or-break difference I'm just going to be ignoring it, as there seems to be little reason to expect it to ever get done.

    I wish I had something more constructive to offer, but I see no point in debating issues in a code that shows little inclination to be implemented.

    1. I should add that if the Phylocode were implemented (or headed that way), I'd have no issue with simply removing the dependency on a particular species concept, although I personally think we shouldn't worry too much about species issue right now - I'm much more concerned with establishing a proper phylogenetic nomenclature for higher levels of taxonomy. The species concept is too embedded and too intuitively obvious (even if on specious grounds) that there is no way it can be revised usefully without a much wider dialogue among biological scientists.

    2. Well, the ICZN took over a century! (119 years if we use the Strickland Code as the starting point; or "just" 56 if we start with the publication of the Leiden Rules.) The Companion Volume is on track to be finished in the next couple of years (possibly next year). If that happens, it will have taken less than 15 years for the PhyloCode to go from initial draft to first publication. Granted, it was originally (naively) supposed to take under a decade, but it's really not that bad.

    3. Given the rate at which communications technology has changed, I don't think that's a very good comparison. The sociopolitical reasons why the PhyloCode has appeal is that it aimed to adopt phylogenetic nomenclature more quickly than the ICZN (and other codes)and it had the potential to unite biological scientists in a single phylogenetic framework, rather than the diverse codes for different fields.

      At this rate, will either of those things be true? The ICZN could potentially start a shift even before the PhyloCode gets published. And what of fields like entomology and botany? They seem to have adopted cladistics (and with it PN) to at a more rapid rate than many zoologists, so will there even be a strong appeal to those fields by the time the PhyloCode gets published?

      I simply don't see 15 years as in any way acceptable in the 21st century, yet that's now the best case scenario. It's time for the "tough love" phase of PhyloCode discussions in my opinion.

    4. A factor of 8 (in the face of active opposition, as you point out) isn't good enough? Seriously? I think people are just disappointed the original "Jan. 1, 200x" was missed. If it had been "Jan. 1, 20xx" from the get-go I doubt we'd be having this conversation. It's all about expectations.

      "The ICZN could potentially start a shift even before the PhyloCode gets published."

      That is hilarious. (Wait, are you being serious?)

    5. No, a factor of 8 isn't fast enough - I got that much of a speed bump in my smartphone over the last 3 years. Besides, what's important isn't a comparison to past events, it's whether the current pace will allow for successful implementation, and the longer this drags on the lower the odds of success get. And I'm not merely relaying my own sentiment, or even that of other outside observers I've spoken with, but even some members on the committee. I admit this is just anecdotal evidence, but that's all anyone has right now.

      I also worry that the odds of success aren't going to decline linearly; if enough people that are high up in the code bail, you could hit stochastic event where the odds basically fall to zero overnight. And for those who aren't yet soured on it, I fear they are too close and don't see the building disillusionment of a lot of outside observers.

    6. That's not a valid point of comparison, because the speed of communication is not directly proportional to the speed of collaboration. (In other words, you aren't publishing multi-author papers hundreds of times faster than researchers from a century ago, either.)

    7. I should have put a winking emoticon after that comment - my point is that the two events (the ICZN and PhyloCode) are not directly comparable because they face difference sociopolitical and technological challenges.

    8. Good. Now publish it.

      It *would* be absolutely hilarious if the ICZN implemented a method for defining taxa using apomorphy-based diagnoses/definitions before the ICPN had a chance to take off. Possibly using Zoobank. Hey, it could happen. ;)

    9. ICZN diagnoses are pretty easily translateable as apomorphy-based definitions, come to think of it! The problem is that the resultant clades might overlap in ways that rank-based taxa cannot.

    10. Unless the ICZN method mandated everything be defined as a grade rather than a clade, which would fit in better with their philosophy. And they wouldn't be immutable, as diagnoses are emended all the time without any formal process.