Saturday, December 13, 2008
Sunday, December 07, 2008
- Michaelson's research. Apparently it has something to do with molecular fluorescence stimulated by lasers. Given that the 2008 Nobel Prize in Chemistry (which I'm sure was picked well after this movie was completed) , did deal with fluorescence, albeit created by Green Fluorescent Protein (GFP) rather than lasers, kudos to the scriptwriters.
- Understanding of how grad school works. This the writers did not do so well. Early on in the movie Michaelson is established as unpleasant and unethical by showing him doing a quickie in his office with one of his grad students who is unhappy with her grade. I suspect the writers only have experience with undergraduate education. Grades just aren't a major issue in grad school. If the student were complaining about her project or authorship on a paper, this would have been more plausible.
- Choice of reading material for a chemist. During the above mentioned quickie, an issue of Cell is clearly shown on Michaelson's desk. Yes, Cell is a major journal -- but for biologists and not chemists. An issue of Science or Nature (which publish across all branches of science) or indeed a chemistry journal, would have been more plausible.
- Amount of Prize Money. The amount "$2 million" is a major plot factor in the movie. But would a Nobel Laureate actually get that much? The prize is currently $10 million SEK (US $1.2 million at present). Plus this amount is shared with the other winners in the category (The movie never says if Michaelson is sharing the award).
Tuesday, December 02, 2008
Monday, November 10, 2008
"how pressure points can help relieve cold and flu symptoms. Learn easy and effective pressure points on the hands, face, and feet to relieve sinus congestion and boost your immune system".I've only taken one immunology course and I didn't recall "pressure points" being mentioned, so I was a bit curious. Looking them up on the web, I find out that they are part of the mysticism behind martial arts! Quoting from that page, I find that
"The Eight Brocades, an ancient Chi cultivation technique that help heal the body, prevent illness and boost your immune system while activating special pressure points. These exercises have been practised for over 1,000 years by Chinese martial arts practitioners."
Wednesday, November 05, 2008
Wednesday, October 15, 2008
Wednesday, October 01, 2008
Sunday, September 14, 2008
Tuesday, August 26, 2008
Friday, August 22, 2008
There's a nice, although small, museum called the "Rainforest Interpretation Centre" that helps visitors learn about the forest through exhibits and interactive displays. One of the oddest things was the three languages used -- English (of course), Japanese (understandably -- much like Hawaii, North Queensland seems to be a Mecca for Japanese tourists), and finally, German of all things! Of course I couldn't resist playing with interactive displays where "Welcher Baum ist das?" was asked. I understand that Europeans visit Australia, but why German in particular and not say, French and Spanish as well?
Thursday was back to science. Craig Cary talked about metagenomics in the Antarctic Dry Valleys -- I hadn't realized that there are ice-free deserts in Antarctica, but apparently there are, and there's cyanobacteria (in particular) living in them. About midway through the talk, Craig shifted gears and started talking about (I'm not making this up) mummified seals! Apparently, Antarctic explorers have long known about these naturally mummified seal corpses (some over a thousand years old) , but Craig was interested in investigating whether the microflora underneath the seals was different than in the surrounding soil. Not surprisingly it was -- the Antarctic deserts are very carbon and nitrogen starved and a slowly rotting thousand year old seal is a much better source of nutrients than anything else around. Craig even transplanted a seal from one place to another to see if he could influence the new environment in the same way, and the experiment worked.
Rick Cavicchioli talked about the genome of Methanococcoides burtonii. I liked that. These days traditional genome projects are somewhat unfashionable (and unfundable), but not everything has to be metagenomics (although Rick is doing that too). Amino acid comparisons with relatives living at higher temperatures were a major part of the story of this genome -- and that work was pioneered by my fellow blogger (and commenter) Neil Saunders, as Rick acknowledged.
I will try to write up a final writeup on the last talks soon. And yes, that is a real live koala with me in the picture.
Tuesday, August 19, 2008
On Tuesday, Phil Hugenholtz talked about his work in metagenomics of a hypersaline mat in Guerro Negro, Mexico. What makes this project a little different from typical "bulk" metagenomics projects such as the Global Ocean Survey is that the peat-like mat has distinct layers of microorganisms even within a centimeter thick sample and these layers can be separated and analyzed individually. Phil and colleagues analyzed 10 layers of the mat and found distinct differences. Particularly interesting was the overabundance of chemotaxis genes on the oxygenic/anoxygenic boundary, which he explained by the fact that microbes that live near the border have to be able to move into their preferred layer as this boundary shifts over the duration of a day. Phil also looked at amino acid bias between layers, which brought back fond memories of my work in grad school linking amino acid differences to thermostability.
Gene Tyson talked about metatranscriptomics, or metagenomics on transcripts (well, cDNAs anyway). As I have a grant funded (with Andy Allen) to do metatranscriptomics on eukaryotic phytoplankton, I found it interesting (although depressing) that despite all the optimizations to avoid it, still 50% of their cDNAs are rRNA.
I had lunch with Rick Cavicchioli and members of his group as JCVI's field biologist Jeff Hoffman hopes to get me involved in the analysis of the Antarctic lake metagenomics data he is generating in collabioration with Rick's lab.
In the afternoon, I presented my poster on "Large Scale Analysis of Nitrogen Utilization Genes in the Indian Ocean" -- basically a bioinformatic analysis of the GOS II data in the context of several genes involved in organic vs inorganic nitrogen uptake and usage. While I wasn't swamped with visitors, a dozen or so people stopped by and gave useful suggestions.
In the evening we had more keynotes from Roberto Kolter and Norm Pace. Kolter's talk (on the genetics of biofilm production in Bacillus) was really wonderful -- and not just for the knowledge imparted -- Roberto is a truly gifted public speaker, a rarity among scientists.
Norm's talk was the same "don't use the term 'prokaryote'" talk that I've heard twice already. Now don't get me wrong -- I have enormous respect for Norm and even quite a bit of agreement for the meaningless nature of the term "prokaryote", but really, I think nearly everybody in the field has either read his paper on the topic or heard him speak on it at least once. This might be forgiven if Norm was some retired scientist who was no longer is generating any new ideas, but happily Norm and his lab are still quite active -- I think everybody would find talks on new work from his lab much more interesting than yet another version of the same "prokaryote" talk.
Monday, August 18, 2008
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.
Saturday, August 16, 2008
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.
Monday, June 23, 2008
Within a span of about six months we have lost two greats with homophonic surnames -- Sam Karlin, the national academy belonging statistician whose pioneering work in computational biology lead to the statistics behind BLAST (as well as more obscure programs), and now the great comedian George Carlin. Many people may think that besides their name, these two people had nothing in common. Not true.
For example, Carlin as well as Karlin has contributed to statistics. Who can forget his great insight "Just think of how stupid the average person is, and then realize half of them are even stupider!"? And before you object that he should have used "median" in that sentence, be aware that the statistical use of "average" need not mean "mean" (in the arithmetic sense) -- the median can legitimately be called an average as well.
And Karlin was a master of the pithy one-liner himself: "The purpose of models is not to fit the data but to sharpen the questions". Well, maybe it didn't bring down the house when he said it, but it's something worth always keeping in mind.
Wednesday, June 18, 2008
Wednesday, June 11, 2008
National Academy member Lucy Shapiro gave a very interesting retrospective keynote on the history of her work on Caulobacter. Having worked on Hyphomonas, a related organism, I found it obviously relevant, but what I found especially interesting was the modest style of the talk. Lucy openly admitted that most of the work was done by her many students and postdocs over the years, and rather than just include their names on an unreadable slide at the end, she mentioned them by name in her talk in the relevant place as she discussed experiments that led to various discoveries about the development and cell cycle of Caulobacter.
Howard Frumkin of the CDC talked about doing "green science", reminding us that biomedical research uses over twice the amount of energy per unit space that the commercial sector does, and that it is important for scientists to "green their sector first" to avoid looking like hypocrites. Although he gave many interesting suggestions to reduce the environmental impact of science, I don't recall him questioning the need for big conferences like the ASM where thousands of scientists fly in from thousands of miles away. Replacing those with video conferences (admittedly much less fun) would greatly reduce the carbon footprint of science.
My ultimate boss, J. Craig Venter, gave a talk about current work in the Global Ocean Survey. Memorably, he started his talk with "I'm J. Craig Venter from an institute of similar name..."
Jonathan Eisen spoke on phylogenomics (link is to Kimmen Sjölander's page on the subject) and origin of novelty, nicely illustrating this rather theoretical notion that he originated with practical examples in his own research. Speaking of Eisen, the picture above was taken at a Red Sox game that I attended with Eisen, Eric Wommack, Jacques Ravel, and some of Eisen's Boston-based relatives. The bearded guy in my picture is Eisen himself, and if you zoom in, you may notice that he has "RecA" written on his hand. Don't we all write the name of our favorite proteins on our hands?
Monday, June 02, 2008
I'll give more detailed information on the talks in later posts, but I'd just like to add to Jonathan Eisen's critique of the structure of the meeting. First of all, it is extremely annoying that they are aren't dedicated poster sessions where the rest of the conference stops -- today, for instance, I had to chose between poster sessions and attending hour long talks by such luminaries as Ed DeLong and Mary Ann Moran, which nearly completely overlapped the poster sessions in time. What's worse, several students of Moran were presenting their posters while Mary was giving her talk, presumably depriving those students of their most interested "customers".
Another exciting event in Boston is that my good friend John Tsang (no, no, not this John Tsang), who was a masters student in the group where I did my postdoc, and with whom I later worked in industry, has just earned his doctorate in biophysics from Harvard. I have to admit feeling a bit of pride in this because I encouraged John to go back to grad school and wrote one of his letters of recommendation. John is going to go through the formal convocation on Thursday, and pictured is John all dressed up (next to his wife Amelia).