noto|biotica

Australia currently has around 100 public biodiversity collections (based on the ALA's Collectory pages), with a combined holding of >50 million specimens covering all organismic groups, and an estimated value of >$5 billion. In aggregate, the collection comprises a megascience infrastructure for biodiversity research in Australia, our region and the world, similar in scale and value to other megascience initiatives such as the Square Kilometre Array or the Large Hadron Collider.

However, the collection is jurisdictionally very scattered. In general, each state and territory has a large or relatively large herbarium and museum collection, under a variety of jurisdictional and reporting arrangements (e.g. from semi-autonomy under an independent Board to embedded in botanic gardens or various government departments). Some universities have collections, ranging from small teaching collections to substantial holdings. There is also a long tail of smaller, special-purpose collections in universities and various government departments. 

This jurisdictional scatter has arisen for obvious historical reasons: the establishment of the major herbaria and museums was mandated or facilitated under state and territory legislation; the CSIRO collections were established under its research mandate; and the smaller collections were established by universities and government departments for specific purposes not adequately covered by the major institutions.

Importantly, funding decisions that affect our collections are made by a very wide variety of budgeting agencies (from local to state or territory to national), with very little national coordination or strategy that can buffer a given collection from the exigencies of its local funding pressures.

Further, the wide scatter of collections means that few "owners" of collections see their collection as part of a megascience infrastructure, and nor does the community as a whole.

So, here's my vision:

By 2028, all our biodiversity collections will be integrated to form the Australian National Biodiversity Collection

The main goal of the ANBC will be to change the way governments, industry and the community view our individual collections - from seeing them in isolation to seeing them as part of something much greater. For obvious reasons, each individual institution will remain under local jurisdictional control and management. However, we will market our collections as e.g. "The xxxx collection, part of the Australian National Biodiversity Collection". 

We will establish an arrangement under the Council of Australian Governments (COAG) whereby the importance of each collection as part of the whole is acknowledged, including if possible negotiated agreements on minimal required baseline funding for each collection. 

We will also establish a strategic governance structure for the ANBC as a whole, to ensure strategic planning for the aggregate as well as individual collections, rather than for individual collections alone, and to increase recognition of the strategic value of each collection and of the ANBC in aggregate, in order to increase profile and funding.

Holotypes are the universal standards we use to build our taxonomic knowledge. Since the integration of genetic data into our methods, our knowledge of diversity is rapidly increasing, but rarely can be linked back to species names. This has led to a divergence of knowledge systems where sometimes we have a parallel set of understanding that cannot be accurately tied together. In order to progress taxonomy, we need to be able to link all this new information with the centuries of foundational work based largely on morphology. Most holotypes are old, or preserved in a way that doesn’t easily allow the extraction of genetic information. However, newer technologies have overcome many of these issues (e.g. formalin preservation, degraded samples) and it should be possible to retrieve a barcode that could link historical type material with molecular studies.

By 2028 we will barcode 50% of holotypes in Australasian collections. This will result in the ability to link genetic information with available names and provide context for interpreting all molecular studies. This will solve some seemingly intractable taxonomic questions, and provide an essential resource for the future. This matters because currently, at best, molecular studies can include material re-collected from type localities, but most don’t, or can’t, since these areas may be highly impacted by human development. The proposed project will provide absolute certainty for contemporary identifications.

While it is not possible to utilise a single gene across all life, the key is unlocking the relevant marker for the groups of interest. Shotgun sequencing can be used to produce barcodes for type material. Shotgun sequencing breaks up DNA into small pieces, which get sequenced in short, overlapping fragments. These are assembled into continuous pieces, which will usually contain the high copy genes that we often use for species-level studies.

By maintaining project-level hubs at the involved institutions, existing databases will maintain the complete metadata record, while a purpose-built (very simple) database could list the species name and collection registration number. Using these two terms in a search of the public database GenBank, where data will be deposited, will retrieve all available data for that type. Other resources required would be salaries for project managers/scientists, a budget for sequencing, and the support of the involved institutions.

This project will increase the utility and integration of existing genetic information and provide absolute certainty of species-level identifications. It will also reduce the need for loaning or handling type material, which in many cases, becomes more fragile with age. This is future-proofing taxonomy!

By Nerida Wilson and Kym Abrams

Here's a wild idea for the Taxonomy 2028 Challenge - some thoughts that came from listening to Peter Raven's talk about the Shenzhen Declaration at the recent International Botanical Congress.

There are two possible scenarios for the future of humankind in the Anthropocene:

Scenario 1: we catastrophically over-reach the earth's carrying capacity, resulting in an uncontrolled crash back to a pre-industrial state (from which we will probably never fully recover given that all the easily accessible fossil fuels are now used up);

Scenario 2: we manage the coming demographic transition in a sustainable way, with population (and resource utilisation) peaking sometime mid-Century followed by a gradual decline in both population and resource use, and with continued increase in our technological capacity.

In either scenario, the Anthropocene will inevitably comprise a mass extinction event. In the first scenario, the living world will come through the mass extinction in much the same way as it has in the past, with diversity gradually rebuilding over the next several million years. 

In the second scenario, we have a more interesting (and optimistic) scenario. After the demographic transition, we will be able to gradually reduce our ecological footprint, and will be able to embark on a phase of "rewilding" the planet - we contract the amount of land we need for food production as we farm more intensively and technologically for a smaller population, which makes land available for restoring wild spaces and the ecological services these provide.

The problem is, we will have lost a significant amount of biodiversity by the time we can start the rewilding.

So here's the proposal:

By 2028 we will have collected and stored tissue samples from all Australasian biota in a genomic ark

Despite the inevitable mass extinction, we act now to store as much genetic diversity as possible in the form of DNA-stable tissue samples. Once the rewilding starts, we will almost undoubtedly have the technological capacity to recreate species from DNA samples, using CRISPR/Cas9 or other gene editing technologies. The limiting factor will be having the DNA material to do this.

So, by 2028 we will have an Australasian genomic ark, the main purpose of which (though not the only purpose) is to store stable genomic samples of as many organisms as possible from our region. This can be done in a variety of ways, e.g. dried leaf samples for plants and tissue samples for animals, environmental samples for fungi, microbes etc.

An interesting issue is that we need to try to sample as much biodiversity as possible including currently unknown taxa. The taxonomy can come later (perhaps even after the rewilding) - we don't need to have the taxonomy all worked out before we sample. We should aim to store as many tissue samples as possible, whether the know what the organism is or not. This has interesting implications for the sampling strategy we would employ for this.

Such an ark could become an absolutely invaluable resource in the future (if we can avoid scenario 1).

Australia is unique in being a large, flat and mostly isolated land mass that has not undergone any major environmental upheavals for tens of millions of years except for climate change (and some coincidental changes in photoperiod and light availability). The plant fossil record is much larger than most people realize and it offers a stunning record of the change in vegetation that is about as extreme as it is possible to imagine for much of the continent (often from dense rainforest to arid desert). A full reconstruction of this would be an amazing achievement, and would highlight the precious nature of the Australian biota and its journey over millions of years. 

This work will result in a data base that will allow for sophisticated reconstructions of the past impact of climate change, the arrival of humans, changing fire regimes and much more. In the best case this will play directly into matters of significant community importance like planning for future climate change and best managing fire into the future. On another level it will provide researchers with unparalleled access to fossil data when utilizing the living flora for detailed evolutionary studies. Taxonomically well-validated fossils are critical for such studies, and are increasingly showing that molecular-derived dates of lineage divergences are often much too young. There is also potential amongst more recent fossils for ancient DNA and chemical fingerprinting of both micro- and macrofossils to better separate out genera and species. Overall this contributes to a stronger integration of the fossil vegetation record with the extant vegetation. 

All this matters because Australia has undergone extreme change in the past 40 million years and is highly vulnerable to future change. By increasing our level of understanding of the past and how it has shaped the present, we stand a better chance to influence what the future might look like. 

Resources to achieve this include smart young researchers who are committed to their own, but also to the collective, good. None of the research required here is expensive, but it needs a new generation of people with research skills that are fast disappearing. It also requires a very sophisticated databasing approach and firm overall control so that data is compatible across all areas. The approach taken should match that used for databasing the living Australian vegetation, but will include the need for better access to modern microscopy (scanning and transmission electron microscopy), automontage microscopy and some of the newer techniques for analyzing specimens such as neutron tomography, which is available at ANSTO. 

Posted on behalf of Dr Peter Johnston, LandCare Research, New Zealand

This includes named species, as well as species known from specimens or living cultures in curated scientific collections, but not formally named.

The IT infrastructure needed to manage this data, analyse it, interpret it, and deliver it in a way that is useful to humans, is available. This interpreted data will be delivered to users in real time and updated as new taxa are discovered.

This will provide:

• a truly robust phylogeny of Australasia’s biota, from population through to kingdom.
• understanding of the Australasian species and lineages that make this part of world special, irrespective of kingdom [e.g. from koala to epacridaceous root endophytes]
• recognition of the species and linaeges that are exotic, prediction of their putative biology, and understanding of their potential risk to Australasia’s economy and inidigenous biota.
• ability to place taxa known only from environmental DNA sampling in the phylogeny, irrespective of the gene or genes used for that sampling.
• important management tool for dealing with the high-risk and unique parts of Australasia’s biological diversity through accurate mapping across space and time, based on national landscape-scale eDNA surveys. 

 Using the potential of microbial diversity in innovative ways:

By 2028 we will be in the age of microbiology, with micro-organisms contributing to the majority of industrial processes.  We urgently need to explore their diversity and potential. 

This will result in using microorganisms and their enzymes to improve human health, increase crop yield, recycle waste products and eventually replace much of the fossil(ised) economy.

This matters, because with an increasing population and increasing demand for animal protein, agriculture must become more efficient, as there are finite resources on earth there is an urgent need to reduce or recycle waste, and a moral requirement to reduce pollution from industry.

Resources to achieve this will be

·         Public support so that people are aware of, and in agreement with, using microorganisms and their enzymes to ensure a more sustainable future.

·         The political will to look forward, by investing in discovery programmes focussed on the microbial communities of Australia in ancient rocks, in highly leached soils, and from the unique flora and fauna that occurs in diverse climatic regions.  These programmes will include not just what is there, but how these organisms are able to survive in such unusual environments.  An outcome with be to determine how this ability can be exploited in novel ways in new industries.

·         Investment from the extractive industries in microbial discovery in low pH and highly saline environments in order to develop enhanced biomining and bioleaching of mineral ores.  This will enable these techniques to be applied to a wider range of materials, under a greater range of physical condition than is possible at present.

·         Investment from the agricultural industries for developing microbial products for the better use of waste products.  An example is the use of fungal enzymes for recycling keratin from animal waste into nitrogen-rich products such as plant fertiliser and animal feed.

·         Investment by manufacturing industries in the use of microbial enzymes to minimise waste and pollution, so that this becomes part of their licence to operate.  Examples are the use of fungal enzymes in the pulp and paper industry, and in tanning leather.

This list could go on….and on….

Elaine Davison

You’re invited to take part in the Taxonomy 2028 Challenge, to help create a vision for systematics and taxonomy in Australasia for the coming decade.

We’d like you to scan the horizon, and share what you see. Where would you like taxonomy and systematics to be in a decade? What achievements or programs would you like to see in place? What milestones would you like us to pass? What innovations in technology, infrastructure, funding or organisation will make a big difference to your work and to our taxonomy and systematics?

An inspiring and ambitious vision for the future is a key element of the Decadal Plan for Biosystematics and Taxonomy in Australasia 2018-2028, which is currently under development (see https://www.science.org.au/support/analysis/decadal-plans-science/biosystematics-taxonomy).  

In thinking about this, please think in concrete terms. We’re after ideas that, after discussion and with broad community consensus, can be included in the Plan as specific objectives (such as projects, programs or milestones of activity) that will benefit both our science and our end-users. We will use these as hooks to argue for more resources, to create more visibility for our discipline, and to foster a more general appreciation and understanding of the value of taxonomy and systematics.

We also need to build the foundation for the next decade (2028-2038), so please think ahead.

The Taxonomy 2028 Challenge will work as follows. Please write a description of your idea. This should be fairly concise if possible, but your contribution could be a couple of lines, a paragraph, some dots points, a blog, or a full-blown discussion paper. Ideas cannot be too big, or too small (though we prefer big). If you have lots of ideas, please write separate pieces for each, unless they go together as a package. There’s no limit to the number of contributions per person.

In order to keep some consistency, please try to structure your contribution something like this:

1. By 2028 we will … [the big idea]

2. This will result in  …., …., …. [the impact]

3. This matters because …., …., …. [the importance]

4. Resources to achieve this will be …., …., …. [the details]

Please try to think in the context of your own work and research group, but also outside to biodiversity in general - the Plan, after all, will cover all of biodiversity. Goals such as “By 2028 we will develop a complete phylogeny of all [.....] in a cool genus beginning with C” may be a little narrow in scope.

It’s probably a good idea to discuss your ideas with colleagues and friends, either before or after you write the first draft.

When you’re ready, please email your contribution(s) to me at kevin.thiele@science.org.au. Indicate in the email whether you’re happy to be publicly acknowledged, or would prefer to remain anonymous.

All contributions will be published on noto|biotica for comment and discussion as they come in. At the close of the Challenge, we’ll analyse all contributions for common themes, and use them for further discussions including for sector meetings later in the year. All contributors will be acknowledged in the final Decadal Plan.

We’re very keen to hear from as many people in our sector as possible; so, whether you’re paid staff, volunteer, associate, or student, whether you work directly in taxonomy or biosystematics, or in associated roles such as curation or bioinformatics, please put your thinking caps on.

We’re also very keen to hear from students and Early Career Researchers (after all, it’s your future we’re talking about). As encouragement, three prizes are up for offer, to a student or ECR who contributes the:

• most popular idea

• most novel idea;

• most ambitious vision.

CSIRO Publishing is dedicated to publishing excellence in taxonomy and systematics, and has generously offered a prize for the winner of each category above. The prize consists of a $100 book voucher, as well as a subscription to your choice of journal (Australian Systematic Botany or Invertebrate Systematics) and free open access for your next publication to one of the above journals. Prizes will be judged for contributions received before 31 August 2017.

So – please do the vision thing, and let’s start shaping our future.

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...

For the last decade or so, Australian botanists have been doing a very interesting thing (we've actually been doing lots of interesting things, but this blog is about just one of them). We’ve been naming taxa (or at least, putative taxa) outside the International Code of Nomenclature for algae, fungi and plants (the Code), using a parallel but carefully formulated and controlled nomenclatural system.

This is the phrase-naming system, standardised by Bill Barker on behalf of the Council of Heads of Australasian Herbaria (CHAH) in 2005 (see Barker, W.R. Standardising informal names in Australian publications, Australian Systematic Botany Society Newsletter 122, 11–12, 2005).

A phrase name is a name constructed under the agreed CHAH standard, with the form “Genus-name sp. Phrasename (Voucher specimen identifier) Source”. Some examples are Acacia sp. Ambathala (C.Sandercoe 624) Qld Herbarium, Sauropus sp. Jabiru (C.R.Dunlop 3381) NT Herbarium, and Typhonium sp. Kununurra (A.N.Start ANS 1467) WA Herbarium.

The phrase-naming system was standardised at the time the Australian Plant Census (APC) project was initiated. This is no coincidence – the APC was an initiative to checklist accepted vascular plant taxa across Australia, and a standardised phrase-naming system was required for that effort.

At first glance, our vascular plant phrase-naming system may seem prosaic and uninteresting - what's so special about putting tag names on plants? However, I reckon it's actually much more interesting than it seems. Firstly, to the best of my knowledge, it's globally unique: no other country has an agreed, formal, multi-jurisdictional standard for naming taxa outside the normal provisions of biological nomenclature. But beyond it's uniqueness, I think it establishes a precedent and a model that could provide much-needed flexibility in naming throughout modern taxonomy and systematics.

Names and namespaces

Technically, names are GUIDS (Globally Unique Identifiers). A GUID is a key (a number or text string) that identifies a thing, and that the system designer can assert uniquely identifies that thing and only that thing within the system. If this is the case, a GUID can then stand in for the thing itself. GUIDs are particularly important in globally distributed systems (like the internet, or biology), where the Globally Unique part of GUID means exactly that.

To ensure that GUIDs are globally unique, a control system and a set of rules are needed, which together control the assignment of GUIDS to things, and the resolution from GUIDS to things. If such a control system is present, and it results in global uniqueness, the system is called a Controlled Namespace. A great example of a controlled namespace is the DNS (Domain Name System), which controls how domain names (like notobiotica.posthaven.com) are assigned and managed. If the DNS didn’t control domain names as GUIDS, and two separate websites could each have the same domain name, the internet would quickly unravel.

Taxonomists around the world are very familiar with controlled namespaces, because that's what the three Codes of Nomenclature (the botanical, zoological and bacteriological Codes) are. The Codes are complex sets of rules that control how names are assigned (rules of validity), are deemed to be correct or incorrect (rules of legitimacy), and are resolved when several valid and legitimate options exist (rules of priority). The rules ensure that one taxon has one valid and legitimate name (that is, each taxon has a GUID). 

The Codes, while exceedingly important, are not perfect, largely because they evolved at a time when controlling the biological namespace was effectively impossible. Taxonomists wore funny wigs, spoke Latin, printed their taxonomy in books using Gutenberg presses, and distributed them by slow boat or a new-fangled and very cool thing called a postal service. If the internet had been invented at that time, it would be a complete mess. The fact that biological nomenclature isn’t a mess (it’s actually pretty good) is testament to the great workarounds that our nomenclatural forebears put in place at the time the Codes were consolidated in the late Nineteenth and early Twentieth Centuries.

As well as being imperfect, the Codes are not magical: they're useful only because of the controlled namespaces they enable. And if good reasons emerge to set up more controlled namespaces, there's nothing to stop us doing just that.

The fourth namespace

This is why I think the Australian phrase-naming system is interesting. It's a fourth controlled namespace. (Remember that it combines a standard rule for forming names, and a process - the APC - that ensures uniqueness, hence the phrase-name system in a formal sense is a controlled namespace.) In fact, while we often call phrase-names "informal", in contradistinction to the "formal" names created under the Codes, in many ways they're just as formal. 

This fourth namespace was created to solve a specific problem in Australian botanical taxonomy, which is that we have a bottleneck: taxa (at least, putative ones) are being recognised in Australia faster than we can deal with them under the normal mechanisms of taxonomy and name them under the Codes. The phrase-naming system was invented as a "parking bay", to enable names to be given to these taxa - with all that that implies for communication, conservation etc. - while they await "formal" naming. It's a neat partial solution to the taxonomic impediment, which of course is what causes the bottleneck in the first place. 

The thing I find interesting about this is that there are many dimensions to the taxonomic impediment, and formal phrase-names established under a controlled namespace, like the Australian vascular plant phrase-naming system, could play a larger role in dealing with these. In a later blog I'll try to draw out some of these possibilities, and to show that this fourth namespace could play a larger and more interesting role in our overall taxonomy than it does at present. It could, for example, be extended to the whole of Australasian biology, allowing the formal (informal) naming of organisms other than plants. In doing so, it could play an important role in rapidly capturing, with unique names, all our taxon concepts, even those that are not yet ready (for a variety of reasons) for naming under the Codes (or indeed, and here's a thought, ones that we have no intention of naming under the Codes).

Coming up next - extending phrase-names to the whole of life, and to more than just "taxa"...

It seemed a logical choice at the time. For a boy growing up with a sciency bent in a small and unremarkable country town in northern New South Wales, it seemed engineering as a career made sense, or so said my rather unimaginative high school careers advisor. Off to the big smoke I went, and 6 months into a chemical engineering degree, I fell in love with .... biology.

Engineering and I negotiated an amicable separation and my new crush led ultimately to a postgraduate degree at the University of New South Wales (Sydney), where I developed research skills and credibility in phylogenetic systematics of plants. After graduating I was off overseas where I worked on the evolution of photosynthesis in bromeliads, using a phylogenetic approach, at the Smithsonian Tropical Research Institute in Panama and Oxford University in the UK.

I returned home to Sydney in early 2000 and after a period of research odd-jobbing (ranging from taxonomically revising a small genus of vascular plants, to working on the genetics of gestational diabetes), I landed dream job #1: Tropical Botanist at the National Herbarium of NSW. A hugely satisfying 6 years of research and practical herbarium taxonomy ensued, until as fate would have it dream job #2 emerged, fully formed, seemingly from nowhere. Strange how the most wonderful things happen when you least expect them.

Dream job #2 is what I do now: Director of the Australian Tropical Herbarium, a joint venture between CSIRO, the Queensland Government, The Australian Government Dept. of the Environment, and James Cook University. This dynamic and growing organisation, located on JCU’s Cairns campus, aims to be a significant global player in tropical plant biodiversity research. My role is roughly equal parts management/leadership and research. The latter involves studies of the origins, evolution and classification of plants and deals broadly with the questions: how many plant species exist, where do they occur, how are they related and how have they evolved? More specifically this research is:

•       discovering, naming and classifying new plant species and determining the evolutionary relationships among them,

•       mapping the distribution of ecosystems, species and genetic variation within species across the landscape,

•       developing DNA-based tools and ‘matrix keys’ for species identification and rapid biodiversity inventory

•       uncovering the deep-time origins and ancient migration pathways of plants that are found in tropical Australia today

I’ve been lucky enough that research has taken me to many biomes and countries including the Republic of Panama, Venezuela, Papua New Guinea, Indonesia, New Caledonia, Malaysia, New Zealand and the United Kingdom.

In addition to institutional and science community leadership and research roles, I contribute to biodiversity and science policy development and implementation through roles on a number of advisory committees and expert panels for the Australian and State governments, and the non-governmental research sector.