16 January 2012

A Proposal to Amend the PhyloCode

The draft PhyloCode has been in a pretty stable form for a while. But recently, there has been a proposal to drastically change how it handles species. You can read the proposal here: 

The first paragraph:

The overarching goal of this proposal is to remove all mention of "species" from the  PhyloCode. Detailed justifications for this goal are given in a supporting paper (Cellinese, Baum, and Mishler, in review); here we present a summary of the main arguments, along with specific proposals for change.

Before I weigh in on this, I'm curious as to what other people think. Please comment below, or send comments to David Marjanović, the Secretary of the Committee on Phylogenetic Nomenclature.

If anyone would like a Microsoft Word version of this document, just ask.

I have weighed in.




    Implement the freaking PhyloCode. Just get it done. Stop tweaking. Make it happen.

  2. Well, fact of the matter is, the Companion Volume is going to take a little while longer. (And it's not going to be abandoned or pushed out.) In that case, it makes sense to sort out any remaining issues in the code. (Assuming you agree that this is a real issue.)

  3. Wouldn't this require scrapping the current companion volume, much of which I understand is written and waiting for publication? Or were CV authors generally not using species as specifiers in their definitions?

  4. Exactly. The fact that commission is even giving this idea headspace fills me with despair. Every moment of PhyloCode-related time should be going into the Companion Volume. I spend a lot of time with rank-based taxonomists over on the ICZN list, and the general impression in that community that the PhyloCode is, if not dead, then dying quietly in a corner. If they now find that we;re trying to change all the rules at this point, they will be in danger of dying themselves -- of laughter.

  5. Mike, We are not trying to change ALL the rules! Please, read the proposal. This is about naming clades that approximate to traditionally named species, just like you would use the PhyloCode now to name clades that approximate to genera, or families. The code recommends retaining (repurposing) the traditional rank names to foster stability so we are advocating to treat species-approximating clades equally, regardless of species concepts. We want to be able to name all clades and have the Code applying at all levels, not just at the genus or family level. If the code is truly rankless, then 'species' has to go too. So, I would leave God alone and realize that this is not a big change after all and it would make sure that ALL proponents of phylogenetic nomenclature are satisfied. This way the code would be truly inclusive. Because, if you don't want to name clades making reference to traditional species you would be free to do so. But if I do want to do so, right now the Code doesn't allow me to. I can only generate references to higher traditionally circumscribed groups.

  6. We seem to be having the same discussion on your blog and Mike's :-)

    To make life simpler, I'll limit my replies to your blog (sorry, Mike!) See you over there: http://cellinese.blogspot.com/2012/01/species-and-phylogenetic-nomenclature.html for anyone who's not seen it.

  7. Hi Mike T. i share your concern about getting the Companion volume done and out (my conscience is clear, though -- my treatments are done). But it is just as important to have the Phyocode be solid and logical. I'm not sure we can avoid ridicule from rank-based taxonomists no matter what, but the real audience are uncommitted students and others just entering the field. The Phylocode needs to be clean and compelling; it is worth fixing up before publication. The Phylocode is about naming clades, period. It is not about naming species or any other other traditional ranked taxa. The proposal we wrote is simple and logical and should not need much thought.

  8. While it certainly IS important to have the code be solid and logical, it's absolutely not necessary to have it perfect in the first draft. You all may have noticed that other nomenclatural nodes have also been amended from time to time...

    ...the important thing is to get the code out officially. We'll likely run into problems that need to be amended anyhow once it sees more widespread use. Launching PhyloCode isn't the end of a journey, it's the beginning of one, so stop letting perfect get in the way of good.

  9. What Scott said.

    (For the record: I was solicited to contribute entries to the Companion Volume on 5th and 12th March 2007, and our team of five submitted them on 17 April. On 15 May we were informed by Phil Cantino that we could cite them as "in press". Now here we are five years later: they're still in press, there is no Companion Volume, there is no PhyloCode and want to make fundamental changes to the draft. Really, I despair.)

  10. If the Code was about to be published I can see the argument, but it is not. We don't even have a date set. may be by the end of the year, maybe not. There is absolutely no reason why at least SOME of our proposals can be implemented. Maybe not all, but some indeed to improve the existing draft. Now it would be easier than later because there is nothing to ratify with the present. This is not a matter of let's get it out. This should be a debate on the philosophical issues, and whether what we are proposing is right or wrong.

  11. OK. I've made my position clear, I won't labour the point by repetition.

  12. Nico, to me it's the mindset. I'm not seeing enough urgency from the people who can set a date (or pressure those who can). The primary issue needs to be to implement PhyloCode ASAP.

    Once the ball is moving in that direction more clearly I'll be able to get back to debating proposals. It's not that I don't think the individual proposals are important, it's that I feel the weight of them (and the lack of action as a whole) threatens to render all of them moot.

    Get the PhyloCode out now!

  13. But Scott, the Phylocode is not near to come out and it won't be out for a while. This is the time to modify it because it would be better and quicker than a formal ratification later, given the Code hasn't been yet published and it won't be out tomorrow or the next month or the month after the next. I want the Code out too, believe me. It saddens me that the issue here is not what we are really proposing but seems to be about timing instead. Yet, the Volume is not ready and so the Code wont be out in the near future.

  14. I agree with Mike Taylor and Scott. While I like the idea of being able to define species as clades and dislike the idea of making all definitions based on specimens, the important thing in my mind is that this would mean rewriting ALL of the Phylonyms chapters and divorcing the definitions from anything proposed so far (except Clarke's 2004 Ichthyornis paper AFAIK).

    The amount Phylocode has been allowed to languish is appalling. January 1st 200N indeed. Now it's 1-1-201N at the least. Just publish it, it doesn't have to be perfect. Give the remaining Phylonyms authors six months to get their chapters in. If they don't, they have no excuse, and that group will just have to be defined in the post-Phylocode literature.

  15. The review process is a bit more complex than that. Even if an author gets something in on time, there's the matter of the reviewer's promptness. And then the author's promptness in making revisions. And then the editor's promptness in reviewing the revisions.

    Phylonyms has already been pared down to much more modest coverage than the initial vision. (Although still significant, with 228 contributions.)

    As a reminder, a status report was posted last September. At that point in time, 100% of contributions had been submitted, 74% had been reviewed, 47% had been resubmitted and accepted by at least one editor, 36% had been accepted by at least two editors, and 4% had been accepted by all editors.

  16. Honestly, I don't care if a single definition gets published in the volume - I want the published guidelines, and nothing of consequence should be holding that back.

    Seriously, I don't think some of you realize how easily this whole thing could be for naught. And then we'd be stuck in a sort of limbo, with the ICZN (and related commissions) not changing fast enough to keep up with modern phylogeny, no unified set of rules, and everyone who already uses PN hacking out a sort of "how I see fit" methodology.

    I don't care that the review process is taking a long time - what are the initial publications but vanity plates for the authors anyhow? Publish the code with the 4% of fully accepted papers (or like Mickey said, place a 6 month deadline - I imagine quite a lot of peer pressure would be placed on everyone to step it up) and publish it with whatever percentage is ready then.

    The issue is much larger than whether or not PhyloCode is perfect, or whether individual groups will get to be defined at the outset - the issue is the future viability of the PhyloCode to serve as the underpinning of phylogenetic nomenclature, and it's dangerously close to being relegated to permanent obscurity.

    STOP IT! Publish the damned thing!

  17. Kevin de Queiroz wrote: "On a related note, several people have reported that they have heard others say that the Companion
    Volume and/or the PhyloCode is/are dead."

    I agree with Mike T., Scott, etc. If ICPN detractors weren't justified in thinking the project was dead after 10+ years in development, a change necessitating a complete re-write will not exactly convince them otherwise.

    If the new proposal goes through, wouldn't the process of writing and reviewing Phylonyms (which has, apparently, been the sole factor holding publication back) need to start again? Any definitions involving species would need to be changed.

    Nico says the code is nowhere near publication. If that's true, it's dead. I second Scott's call to just publish it already. Otherwise most people, even supporters, are going to start writing it off and focusing on other options.

  18. "just publish it already"

    Amen! I have been saying this for literally years.