Monday, July 25, 2011

Taxonomy as Wastewater Treatment

I was thinking about taxonomic treatments of specific groups of organisms; in some cases a 'treatment' is essentially a rehash and synthesis of what has been published previously (but just for a specific subregion, etc). While focusing on the mechanistic details of how my colleagues and I put together treatments (not through rehashing), I thought of the process by which sewage is treated. So I did a Google image search for "taxonomic treatment," and basically got a bunch of photos of journal pages/covers, some phylogenetic trees, and some photos of organisms. I think that's pretty much how most people see biological taxonomy, which explains a lot about why taxonomy is often seen as dull and sometimes (even worse) unscientific. But then I did a Google image search for "wastewater treatment" and I was amazed to see that the images there generally matched my concept of how to do a taxonomic treatment much better than what I saw in the previous search! What I saw were mainly flowcharts... they showed processes like screening, pre-treatment, cleaning, clarification, digestion, storage, disposal... and the processes all flowed into one another and ended up making products for public consumption! Yes! This is it! This is how we really need to be doing taxonomy! Instead of perpetuating the problems that exist, take them head on... get the junk out of the way, and make something that people can use. Many researchers seem to be of the mind that if it's mostly right, it's good enough; but as any wastewater treatment plant manager will tell you, even if it's only 10-20% sewage, it's not fit for public consumption. Let us view our taxonomy in the same manner!

Lichenologist James Lendemer is famously quoted as saying "I think of myself as a bounty hunter." Perhaps I should think of myself as a manager of a wastewater treatment plant. Maybe that's not as glorious, but it certainly is important. So much work remains to be done before we get close to having a reasonable set of names for the organisms on the Earth. As long as humans are involved, our nomenclatural system will be imperfect and will require constant cleaning, management, and enforcement of standards... and there I will stand, ready to take on the nastiest and dirtiest of the problems!

- Brendan

P.S. Some recent big news in the NYC area has been the big fire at a wastewater treatment plant that sent sewage spewing into the Hudson River. Thought exercise for taxonomists: Can you think of any events like this one (speaking metaphorically) that affected your particular group of organisms?


  1. Molecular phylogenetic studies have always been enigma for me. How can one person make a conclusion that two organisms are close or far relatives comparing tiny part of their genome?? It is very funny when I read in Lichenologist (and other magazines) articles with big charts showing branched "relations" among species and based on these data placing them in certain genus. Does those who write these articles mean it seriously? :)

  2. Although I'm obviously a big proponent of molecular phylogenetics, I think I understand your sentiment. There are so many problems that can arise along the way to a phylogeny in so many areas: improper identification, contamination, etc. Then there are the issues that are more philosophical in nature (or course blindly following a certain philosophy can lead to a non-sensical taxonomic system). For example, just because two organisms make a single clade based on a certain reconstruction with certain genes, it doesn't mean that they should be grouped in the same genus if they do not have morphological features to unite them. There are also many issues associated with properly reading phylogenetic trees. It is clear from some articles that authors misunderstand what a specific tree indicates about the history of a set of organisms, which can lead to many taxonomic changes that make little sense from a holistic perspective. From my perspective, the best approach to defining taxa is to look for correlations between different data sets (e.g., chemical, morphological, molecular, biogeographical, ecological), instead of relying too heavily on any one data type.

  3. An enlightening pledge to other phylogeneticist-to-be. Working on molecular phylogenetics myself, I always wonder the significance of my work, that is, why is it so important to unravel the relationships between different organisms which do not seem to hold any economic importance, apart from contributing to the database of knowledge? Perhaps I've not been trained enough to think out of the box. I am glad to have came across your blog :)