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Michael DuVernois | Wisconsin IceCube Particle Astrophysics Center | USA

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PACIFIC 2012 and the Dark Taxa

Well, this is a bit of a late posting for me, but it’s been a crazy few months with a house sale, house purchase, daughters starting high school, and a frantic build of two stations for the ARA (Askaryan Radio Array) experiment that we’ll deploy at the South Pole this Austral Summer. More on most of those topics soon, but a little report on the PACIFIC 2012 conference and some biology that I learned while I was there. (Any and all biology in this article is as reported by myself, an astroparticle physicist, so apologies to actual biologists, this is posted out of “hey, that’s neat” intellectual curiosity and not some sort of physicist supremacy theory.)

So, the PACIFIC 2012 conference was held in early September in beautiful Moorea in French Polynesia. I felt pretty guilty heading to a meeting in paradise, so I did my best to bring back some gifts… It’s an annual, small meeting on particle astrophysics and cosmology, held at the Richard B. Gump South Pacific Research Station run by the University of California-Berkeley. The meeting was especially interesting to me with the small group of scientists there, in a relatively isolated environment, and with a good mix of experimentalists and theorists. I gave a talk on the IceCube experiment (talk is post here, NB: large file and somewhat technical), including some recent results on the gamma-ray bursts and also a few of the first bright (PeV) events seen by the telescope.

I did manage to find some time to go snorkeling during the meeting. There were a lot of fish and sea creatures in the protected reef waters of the lagoon, and in fact Moorea featured in a recent National Geographic magazine article exploring the living content of a cubic foot of the coral reef. It’s a ridiculous variety and density of life, teeming life in great numbers of species and individuals, in every corner, every niche of the Earth. But, if you read why Moorea was chosen as one of the locations (in work performed at the Gump Center) you find it’s because the isolated French Polynesian islands (it’s a really long flight, and look at it on Google Earth, far from the US, Australia, New Zealand, Asia, and Hawaii) have the least biodiversity on Earth.

Basically, it’s a really long way from everything else, and relatively few species (comparatively!) got there, established themselves, and evolved in place. So, in a manner that a physicist would approve of, Moorea can be used as a simple model of an ecosystem for systematic study. It’s far simpler than most other ecosystems, and many of the species present have their time and method of introduction to the island known. Some arrived with the Polynesian voyageurs, others with colonial masters, and others as accidental tourists in the jet age.

Okay, so you have simple system that you’re going to use as a template for more complex systems later, and maybe one of the first things that you want to do is catalog the species present on the island, in the soil, and in the lagoon. The Biocode project at Gump tries to do just this. Identify all of the species. Since I last took a biology class of course this is not just a process of identifying the species by its characteristics (Wikipedia background on taxonomy) but also via the DNA characterization of the species. (I must put a call out here to the brilliant DNA analysis work on restaurant sushi. Check it out if you haven’t before.) In fact, increasingly the species being discovered aren’t being formally named, or even identified in the sense of “here’s a canary, you can tell by its song, and this brilliant plumage” but rather by the existence of a unique DNA sequence.

For example, you can identify all of the critters you can (in Moorea, down to about a couple of mm in length), record their DNA, and then take the contents of a fish stomach and sequence that DNA. In the stomach you find the DNA of species that you had not previously identified. In fact, it seems that many, or most, species do not have a catalog entry, a sample pinned onto a board in the basement of the natural history museum, they just have some DNA in the instrumentation in the laboratory. These are the dark taxa, genetic information without the classical context of the detailed, properly named, taxonomy entry. The name is nicely analogous to the Dark Matter. Most of the mass of the universe is not in ordinary, observed matter, but in a “dark matter” which interacts gravitationally but is otherwise not observed directly (yet).

The Dark Taxa was introduced by Roderic Page who was considering the entries in species catalogs and noting the explosion in the number of species identified only genetically, with no classical taxonomy. Estimates seem to vary, but perhaps 90% of the animals (let’s not even think about the bacteria) are unknown. The already plenty-amazing world is that much richer still. Most species are unknown, and in fact the definition of species and broader classifications are moving rapidly with the ability of genetic tools to make a more reasonable “a is closely related to b” based on evolutionary distance rather than appearance. The Biocode effort on Moorea was making use of large scale databases, sequencing everything biological that the researchers could find on the island, and working through the classifications via software. It’s a very different biology than I recall from class, more analytic and less descriptive. I hesitate to mention the perhaps somewhat similar division between classic descriptive astronomy (“twelve barred spiral galaxies”) and astrophysics (“we modeled the bar formation with a 3-D hydrodynamics code”) but it does have some of that feel.

Okay, so I went to a tropical paradise, talked physics, and got pretty excited about biology, in particular biological classification. It was a good trip.

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