2005 IRISH SCIENTIST YEAR BOOK

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Martin Ryan Institute, NUI, Galway
Michael Guiry
AlgaeBase – listing the world's algae

They say that information is power, and it is probably true to say that the ability to retrieve information quickly and coherently is even more powerful.

Science Foundation Ireland (http://www.sfi.ie) has identified Information Technology as a prime technology in empowering Ireland well beyond the current Celtic Tiger phase and is investing heavily in research in this area, including a project at NUI, Galway's Digital Enterprise Research Centre ( http://www.deri.ie ) to research the next generation of smart web browsers. These will be better able to sense what the user wants and distil the enormous complexity of the web to something that is instantly useful. AlgaeBase is doing the same thing – it is trying to bring order and sense to a hugely complex world of information on algae.

The building blocks of communication in biology are names. Love 'em or hate 'em, these Latin and Greek names are simply a way of communicating what we know about organisms. The science of ordering these names in a coherent way that reflects their evolution is known as taxonomy. We have developed a complex set of rules to decide how we order these names, known as nomenclatural rules, which is agreed internationally under a Botanical Code, a Zoological Code and a Bacteriological Code. All are similar in some ways and quite different in others and have given rise to another science, nomenclature, which relates to the rules that we have agreed for names. To the outsider, there seems nothing more irritatingly petty than some of the rules of nomenclature!


Many mathematicians now say that there is no such thing as true chaos – that everything is ordered, although it is just not always easy to see the ordering principle. Looking at the names and systems put in place for an estimated 1.6 million species in the world, one wonders. Taxonomists often seem to be completely at odds with one another and Joe Homo sapiens Soap might be forgiven for muttering "A plague on all your taxa".

Worry not, dear reader, for the internet rides to the rescue. Instead of spending a life accumulating rooms full of dusty books (and handwritten notes from the ones you can't afford), and making and tending drawers full of card indexes, it can all be done digitally. Put your stuff in a database, and store it all on a computer, where you can retrieve it easily and quickly.

Next step: why not make it available to other people? Well, that is easy too. The current simplicity of the web and its openness (and anarchy) lends itself to instant publication of databases. And this is exactly what we have done for algae.

I'm a marine botanist and my area of interest is taxonomy and biology of marine algae, particularly red algae. In 1996, I started to put information about common seaweeds of Ireland and north-eastern Europe on the site http://www.seaweed.ie . Much to my surprise, it proved very easy to make a database engine to run that part of the site. So, like Topsy, AlgaeBase grew from a seaweed database for the north–eastern Atlantic and Mediterranean to a seaweed database for the whole world. It then became apparent that the attached marine and brackish-water algae could not be isolated from the freshwater, terrestrial, and subaerial algae, not to mention the freshwater and marine phytoplankton.


So, we started to list all the algae. To date we have entered about 65,000 names, of which about 30,000 are currently accepted species and AlgaeBase has grown into a Global Species Database; in other words, a database that includes nearly all of the species in the world. This is the only GSD based in Ireland and confirms Ireland's role as a key provider of biodiversity information. AlgaeBase represents Ireland on several international biodiversity groups and is widely regarded all over the world as the authority for information on algae. Users from many countries including those as diverse as USA, Spain, Mexico, Taiwan and Turkey, consult this Irish resource to check taxonomies or nomenclature, to find out about distribution or to look at pictures. We are also consulted by groups wishing to establish GSDs for their taxa or seeking to discuss current best practice in the field.


Furthermore, we have used the open-source database MySQL ( http://www.mysql.com ) to write a very structured, open and rapid structure that will be extremely adaptable to future development. The interface to the database is browser-based and with a username and password, experts on particular groups all over the world can access the data and make changes. We are setting up groups of "shepherds" that will tend to "flocks" of algae, be it a whole phylum, order, family or even a genus. It is here that the beauty of the internet becomes apparent – a taxonomist can sit in the comfort of his or her own office and at a favourite operating system or machine and contribute to a collaborative project that helps people all over the world.

Nevertheless, there is an inherent conflict in what AlgaeBase does, and it is one that in some ways plagues the internet. Nothing included is truly fixed. When one publishes a book, the information is fixed on the paper and does not change over time (well, until the book rots). The upside is that one can cite a source like this easily; the downside is that the information cannot be updated. With web sources the converse is the case. In the case of AlgaeBase and other Global Species Databases, the data also need to be spread as widely as possible by making mirror sites, providing datasets for World Species databases, and storing data in various ways.




Funding

For the last five years AlgaeBase has been generously funded by the Higher Education Authority under the Priority Research in Third-Level Institutions Programme. We are also the coordinators of a European Union FP5 project called SeaweedAfrica ( http://www.seaweedafrica.org; see page 76 ).

However, existing funding ceases before the end of 2005 and activity will slow down considerably after this. It does not seem possible that the present staff will be retained unless funding becomes available. The replacement of equipment and funding of programming will not be possible without a major sponsor. Unfortunately, if this current situation persists a valuable asset to the Irish biodiversity community and Irish science will quickly begin to become obsolete and lose its footing on the world stage.





Some organisations using AlgaeBase data
At present, AlgaeBase is the accepted authority that contributes algal data to the organisations shown here:
Global Biodiversity Information facility http://www.gbif.net
Species 2000 http://www.species2000.org
GenBank http://www.ncbi.nlm.nih.gov/Taxonomy/
Ocean Biogeographic Information System (OBIS) http://www.iobis.org
Species 2000 Europa http://sp2000europa.org
European Network for Biodiversity Information http://www.enbi.info
Codes for Australian Aquatic Biota http://www.marine.csiro.au/caab/caabsearch-frames.htm
Marine Biodiversity and Ecosystem functioning (MARBEF) http://www.marbef.org
Main phyla of algae represented in AlgaeBase are shown in the table below. (Asterisked phyla are often included in the Protozoa. The Cyanophyta are considered to be bacteria.)



What are Algae?

The answer is a little disconcerting: algae is a generic term for a number of supposedly primitive, seemingly plant-like, generally photosynthetic organisms, that generally form spores of some kind and that are scattered amongst at least four Kingdoms: Bacteria (cyanophyta or cyanobacteria), Plantae (green algae, charophytes, etc.), Chromists (brown algae, diatoms, etc.), and Protozoa (dinoflagellates and euglenoid flagellates), and fall into two Empires (Prokaryotes and Eukaryotes). Actually, the term algae is pretty meaningless in the face of this extraordinary diversity. Nevertheless, it is a term of convenience as most people in the scientific world know to what you are referring, although their mental picture may be sort-of-plants that are not flowers, not mosses, not ferns, not fungi, and not primitive enough to be viruses or bacteria. All pretty negative, but then an expert is probably the worst person to ask.
Some algae are of huge importance to the climate, such as coccolithophorids that may form open-ocean blooms the size of Co. Galway, and it is widely recognised now that, contrary to previous estimates, most carbon is fixed in the sea, and most of this is fixed by algae, many of them very tiny things called picoplankton. Other more familiar algae such as seaweeds also affect the climate by producing DMS (dimethyl sulphide) and iodine, both of which are responsible for the nucleation (seeding) of clouds.
Contact: Professor Michael D. Guiry, AlgaeBase Centre,
Martin Ryan Institute, National University of Ireland, Galway
E-mail: [email protected]