Why Australia's plant phrase-naming system is more interesting than it seems (Part 2)

In Part 1 of this blog (please read that first if you haven't already) I established (I hope) that the system we operate in Australia for phrase-naming vascular plants is an interesting and noteworthy initiative, and one that could perhaps be extended and explored as one part of a solution to the taxonomic impediment (the name we give to the problem that there are not enough of us and we don't have enough time to name all the organisms we need to name). 

I made a claim that the phrase-naming system has all the requirements to be regarded as a Controlled Namespace, and in fact runs parallel to, and augments, that other great controlled namespace, the International Code of Nomenclature for algae, fungi and plants

The purpose of this blog is to make two arguments, firstly that we should consider extending the phrase-naming system to all biota, and secondly (and probably more controversially) that we should explore using it to name aspects of biodiversity that are worth naming, but may not be "taxa" (whatever they are).

Extending the phrase-naming space to all biota

Botanists in Australia created their formal phrase-naming system for two reasons. Firstly, we inhabit a mega-diverse country with a partially documented biodiversity, and are all aware of "good" taxa that, despite not yet having a formal name, nonetheless are in need of recognition and protection. Secondly, and because of this, at the time we commenced work on the Australian Plant Census (APC) project, it became clear that if we included only formal names, we would mis-estimate our plant biodiversity. An intent of the APC was to harmonise taxonomy across state borders, and harmonising phrase-names is just as important as harmonising formal names. In these senses, the phrase-naming system is a simple solution to a practical problem.

The problem that we faced is not unique to botany. In many other taxonomic groups, we recognise more taxa than have yet been named. Collections with large numbers of un-named species are often partially curated using taxonomic "sorts", either physically in the collection, electronically in databases, or at least in the minds of the curators. If an important task of taxonomy (arguably the most important) is to document all known biodiversity, then these "sorts" represent documentation that's currently pretty undocumented.

A practical problem with documenting these undocumented taxa is that they are currently (except for plants) named using Locally Controlled Namespaces, or worse, Completely Uncontrolled Namespaces. If something in a collection is called "Fly sp. 1", there's not much to go on for anyone trying to understand the taxonomic concept concerned. If another collection also has a "Fly sp. 1", and if there's reason to believe that "Fly sp. 1" ≠ "Fly sp. 1", then we have a problem. This is exactly the problem that GUIDs (taxon or phrase-names) are designed to solve.

Just as with plants, capturing and rationalising these names so that we can assert (likely) equivalency between specimens having the same phrase name would be an enormous step in our task to document Australasia's biodiversity. It would give us an opportunity to capture all our knowledge, rather than just the part that's made it through all the hoops to formal naming.

Of course, this statement will immediately raise an objection in the minds of some readers. How can we be sure that these phrase-named taxa really are taxa, if we haven't yet done the taxonomic due diligence that comes with formal naming. An answer is that we work on a sliding scale, and we can't really assert anywhere along this scale that we're absolutely sure that taxon x is really a taxon. There are many cases where we can be as confident that an un-named taxon is a good taxon, as that a named taxon is a good taxon. While there will always be some uncertainty, I don't think we should let that stand in the way of a more efficient and effective way of documenting our biodiversity. 

So - I propose that, as one of the initiatives under the Decadal Plan, we extend the formal phrase-naming of Australasian taxa to all biota, and that we initiate a campaign to capture all of our current taxonomic knowledge, including knowledge that for various reasons hasn't yet made it through to formal naming. The following steps would be needed:

  1. the adoption of a single agreed convention for phrase-naming informal taxa throughout the biota (I'd like to propose the vascular plant phrase-naming convention as a bloody good start);
  2. the initiation of a campaign to capture within the agreed phrase-naming system all taxonomic knowledge represented in our collections and data systems; and
  3. commencement of a system of rationalisation between collections so that over time we can be confident that the same phrase names apply to the same taxa throughout.

Extending the phrase-naming space beyond taxa

I've described the current vascular phrase-naming system as being akin to a parking lot for taxa that await formal naming. This need not necessarily be the case, however. 

If, as I argued in Part 1 of this blog, a phrase-naming system is effectively a Fourth Namespace that sits alongside and parallel to the three existing nomenclatural Codes, it follows that we could design that namespace to do whatever we want it to do. If there are cases where we'd like to name something (i.e., do taxonomy) but we believe this is best dealt with outside the Codes, then we can design a controlled namespace from scratch and optimise it to deal with these cases.

This is where my idea of an all-biota phrase-naming system may get controversial, and I may get shot down.

Nature is immensely complex. Evolution has generated patterns of variation that are among the most challenging in the universe. Given this, is it likely that a one-size-fits-all approach to naming this pattern (one or other of the Codes depending on one's organismal group) is going to be adequate for the task?

Consider genetics and genomics. These immensely powerful tools allow us to discern patterns at a level of resolution and detail never before dreamed of. Having discerned a pattern, there's a strong desire among those of us with a taxonomic bent to want to name entities that we can discern from the pattern. If only one controlled namespace is available, that's the one we choose to name under. I think there's a danger here - that we'll bugger-up a perfectly good naming system that can't, or shouldn't, need to cope with all this extra detail.

This is one reason why I worry about "cryptic species" (I put the phrase in quotes because too often it's written without, thus rather prejudging the whole issue). Let's say that we have a lineage that's morphologically recognisable. Let's say that it was a species that currently has a name (probably dealt with using classical methods). Let's now say that genetic and genomic studies reveal well-characterised sub-lineages, which are not currently recognised in our taxonomy. Having discovered these cryptic lineages, we're tempted to name them as "cryptic species". 

This is all well and good if the point of naming is merely to document biodiversity by boffins, for boffins. The problem is that there are many more non-boffins than there are boffins, and many of these comprise "the public". I believe we ignore this at our peril. Jenny Citizen used to be able to recognise this species, but is now faced with half-a-dozen "cryptic species" that she can no longer discern. If our naming system gets loaded with taxa that she can't understand and can't see, then we'll lose her to our cause. This, of course, would be dangerous to our cause.

If there were only a small number of these awkwardly cryptic taxa, then the system would probably cope OK. If however, there are many, then loading up our taxonomy with names that are effectively useless for many (though not all) users, is a problem. My fear is that the more we look, the more cryptic variation we'll find.

And this is where the Fourth (or Fifth, or Sixth) Namespace comes in. We could design a namespace that's optimised to allow us to capture names of things (such as morphologically cryptic lineages) that we choose not to name in our Code-based namespace. Because our new namespace is a controlled one, it would still serve perfectly well for communication among the boffins and other rare breeds who need it. Our Code-based namespaces, which perhaps are more public-facing, could then be immune from being over-stuffed with these things. 

This would also have the advantage that we'd solve a current problem even for us boffins. Many researchers who discover lineages (or sub-lineages) using genetic and genomic methods, fail to name them under the Codes because they find it too hard. There's a curiously anachronistic view around that you need to find some morphological difference (any morphological difference) to be comfortable to name something under the Codes. A result is that some people work away trying desperately to squeeze some minor morphological difference out of their poor creatures, then (if they get lucky) name them on that basis. Others either give up, or don't bother. The result? Our worst enemy - an uncontrolled namespace. How many Clade A's can you think of in your group's literature? We could invent a system that works better than this.

So - I propose that we investigate a phrase-naming system that will allow us to name genetic lineages and other entities that should be named, just not under the Codes.The following steps would be needed:

  1. the adoption of an agreed convention for phrase-naming genetic lineages (and perhaps other entities such as significant populations);
  2. the establishment of standards for journal papers that will provide a convenient way for such names to be coined; and
  3. the establishment of a system to track and document these names, and that would allow them to be resolved back to an original source.

We could then inhabit the best of all possible worlds (well, that might be going too far), with several carefully controlled name-spaces each optimised for different uses. The sum of our taxonomic knowledge would be the sum of these namespaces, in whatever combination is most fit for purpose for the particular questions asked. I think this would give us much-needed flexibility, that is currently lacking in our nomenclatural system.

Over to you for comment...

4 responses
I love the phrase name system, complete with its flaws. I have been trying to convince our US cousins to implement it there to solve many issues. What it killed is the Fly sp 1 not equalling Fly sp 1. As a younger thing there was a species that was listed under 3 unpublished names: Hova sp 1 (Qld); Hovea sp K(NSW) & Hovea sp B (Vic). This nightmare has gone. The system is not perfect & we do have duplication. A number of arid phrase name taxa that span WA & NT have two names, but that is so easy to fix at formal publication & as is done in Nutysia to publish a short communication clarifying issues. The best is retention of knowledge outside the researcher. If the researcher notes entities, creates phrase names, but unfortunately dies (for whatever reason), the next generation of botanist doesn't have to re-invent the wheel to make progress.
I'm going to be schizophrenic regarding your Third Namespace concept. The metaphysical argument has value. It might be very useful for small character difference differentiation (although we do have the taxon level forma that would cover this). I am not comfortable with your argument regarding cryptic species and Jenny Citizen. My preferred option would be a better, fun education platform that showed WHY it was difficult & that it was difficult for everyone. This is US having control of knowledge & science theory, rather than the public having control of how we do science process. Letting Ms Citizen determine how we formulate final outcomes is flawed. The resistance to change & new theories would be challenged at the micro-level, with us doing incremental changes that each step look like nothing, but could have far-reaching issues. These same micro-steps are how the Christian Right have managed to convince so many average American citizens that the Bible is fact, and that scientists are evil & have corporate agendas & are a drain on the public purse. Remember the clean coal programme, if you were in any doubts. Cryptic species are a pain, but they fulfill a knowledge gain and I think we need to work out smart ways to inform the public. Chris Martine of Bucknell Uni PA is doing great things with his series Plants Are Cool. His courses are full, he never has a shortage of students, and the media hound him for new stories about those crazy plants he works on - coincidently they are Australian Solanum. We need to be inventive as well, so inventive that Ms Citizen & her cohort become an army that lobbies the government for more resources spent wisely to kill and reduce the taxonomic impediment and make us the Lucky Country of the 60s & 70s (research & funding speaking).
For those who think about a similar controlled namespace in zoology, check out Mark Harvey's presentation here: https://www.ala.org.au/wp-content/uploads/2016/... This presentation finishes with "Can it work? I don't know - I doubt it", and I am of an entirely different opinion. We have been using a controlled namespace for terrestrial arthropods "with more than six legs" (i.e. arachnids and myriapods) very successfully in WA. This linked unpublished taxonomic research with end-user (mainly consulting companies) needs, and the use of the system in environmental survey reports (or at least 'a' system used by the WA Museum) is now requested by regulators (i.e. the EPA). We all realise that we will not be able to document our biodiversity within the traditional name spaces and long publications times attached to those. The introduction of an Australian controlled namespace for all biota is, for me, one of the most important steps, possibly the most important step, towards advancing our biodiversity knowledge. However, I would at this stage, advise not be too philosophical about it. Establish it for the same concepts we currently use our 'official' namespaces for, i.e. predominantly morphological species (however, the WA Museum system is also applied to molecular species). This will cover the majority of biodiversity as we currently recognise it and will not frighten J. Citizen. Let a species be what it is, a hypothesis, which works for most end-users fine. We all know that speciation is ongoing and sometimes defining a species is difficult.
1 visitor upvoted this post.