ISME 12 Cairns - Highlights of Sunday and Monday

The first two days of ISME went quite well. First of all, I have to give the organizers high marks for actually providing a conference bag worth having (BTW, it would be interesting to figure out someday where and when the custom of "conference bags" started -- why does every conference assume that attendees need a conference-specific bag?) Rather than the nearly useless tote bags which one often gets, the ISME 12 bag is a nice high quality backpack that will be worth keeping after the conference. Conference bags may be a minor issue, but a quality bag is a nice touch.

Bo Barker Joergenson gave a nice keynote on Sunday night on the subject of the "deep biosphere" by which he means microbes living deep in the sediment at the bottom of the ocean. Ships have returned drilled cores even from a couple of kilometers down that contain microbial cells. For many years there was debate over whether these cells were actually alive or just the "corpses" of cells that drifted down and never decayed, but now there is general agreement that there are living cells. What there isn't agreement at this point is what type of cells there are. Some groups, using Q-PCR have concluded that the primary players are bacteria; others using FISH-IPL say archaea are. As a bioinformatician, I find this conflict of experimental methods disturbing. Still, the "deep biosphere" is a fascinating topic to me.

After the keynote we had appropriately Australian entertainment; a group of local indigenous Murri demonstrated some traditional songs and dances and the use of firesticks.

On Monday the main series of talks began. Curtis Suttle talked about inferring the host species of marine viruses through phylogeny. He began with some fascinating statistics; there are 10^30 viruses in the ocean, and if they were laid end to end, they would stretch for 10^7 light years! And they contain more carbon than 75 million blue whales. So what exactly are these viruses infecting? Suttle has developed an interesting method where he first calculates phylogenies of viruses with known hosts, calculates the average genetic distance between viruses that infect the same host, and uses this distance to cluster sequences of viruses that infect unknown hosts. He then looks for correlation between occurrences of members of these clusters with morphologically different hosts in micrographs to assign presumed hosts. Obviously, morphology is a crude measure of species in any set of organisms (and particularly so for microbes), but it is a useful start.

Forest Rohwer, probably the best known researcher of marine viruses, gave a talk about many different projects his lab is pursuing. What I found most interesting was his idea of measuring the energy usage of phages by measuring temperature in calorimeters containing bacterial cultures with and without phages.

C.D. Long presented a good example of what I find most interesting in science -- the application of a technique developed for one problem to a different one. In this case, she utilized the traditional "checkboard" method (developed by ecologists studying island biogeography) to analyze the co-occurrence of different microbial species living on human teeth. I'll have to read up on the method to see if maybe I could do something similar.

And Mitch Sogin presented on his idea of the "rare biosphere" -- the idea that most microbial species are very low abundance organisms. I've heard Mitch talk about this idea before, but this talk was more technical and included more details --- not only of his experimental methods but also of his VAMPS analysis system. I've spent a lot of time basically writing my own version of many of the methods there because I didn't know the system existed.

P.S. Qantas found Lisa's bags.

ISME 12 in Cairns, Australia

I realize that I've been a non-blogger as of late, but on the off chance some of you still have me in your feeds, I'll try to write something about the ISME (International Society for Microbial Ecology) meeting that starts this evening in Cairns (Northeast Australia, near the Great Barrier Reef).

Getting here was a bit of an adventure; coming into Sydney we were instructed that we must go through customs and retrieve our luggage before continuing on to any domestic flights. So I dutifully did that and waited for my luggage to show up at the carousel. It didn't. It turns out that because my Sydney-Cairns flight actually was the first jump in a Sydney-Tokyo flight, it didn't count as a "domestic flight" and I was actually supposed to go through customs in Cairns and collect my baggage there. After all this was figured out I very nearly missed my flight to Cairns -- as I raced through the Sydney airport to the departure gate I was one of those annoying passengers that you hear getting paged for the last call for their flight. But I made it -- and so did my luggage-- which is more than could be said for my friend Lisa's -- she still doesn't know the status of her baggage and whether it is lost for good.

But here we are in Cairns. As Lisa notes, the city is much like the San Diego that we left from in look and weather. Well, maybe how San Diego would look if Canadians had built it or something -- it does have the distinct Commonwealth feel somehow that I recognize from my time living in Canada.

More posts (with pictures and actual science) will follow.

In Toronto for ASM 2007

This year the big meeting for the American Society for Microbiology is in Toronto. Which is odd, because Canada has its own professional association, the Canadian Society of Microbiologists. Are they going to hold their meeting in New York? Anyway, I'm here and enjoying a return to a city that I visited several times as a teenager and then as a postdoc in the (relatively) close University of Waterloo. I'll try to post highlights as I see them from the conference each day until Friday.

Oh, I have to tell you an amusing story that occurred when I was going through customs today as I was entering Canada: The customs official asked me why I was entering Canada and I told him that I was attending the microbiology meeting, and he asked me where I worked and I told him I worked at the J. Craig Venter Institute, and he responded with "You know, are they ever going to do studies of the ocean bacteria that live too deep for photosynthesis?". Which is a totally valid question -- the Global Ocean Survey used samples collected from Craig's yacht, not a research vessel, so the samples were from the surface. But I was a bit stunned hearing it coming from a customs official!

Concerning the pictures -- one is of Dundas Square -- which didn't even exist the last time I was in Toronto, and the other is of the so-called World's Biggest Bookstore. I went there today for old-times sake. It is quite a large bookstore, and I was blown away by it when I first visited it in the 1980s, when my idea of a bookstore was a typical Waldenbooks or B. Dalton's. But while it's still larger than than the average Barnes and Noble (or Chapters or Indigo, eh?) location of today, it isn't mindbogglingly larger.