Tuesday, May 29, 2007

Craig Venter "plays God" on international editions of Newsweek

Apparently, on European, Asian, and Latin American editions of Newsweek this week, Craig Venter (my ultimate boss after about three levels), is shown looking, I suppose, reflective about the potential awesomeness of synthetic biology and the possibility of "playing God". Or maybe he just has indigestion. Anyway, the article is here. Interestingly enough, neither the cover nor the article appears in the US edition. The article is interesting enough, but I wish it would have clearly distinguished the public research on synthetic biology going on at the JCVI from Craig's startup. Yes, both involve Craig, but not everyone who works for Craig is on the private sector side of things.

Friday, May 25, 2007

ASM 2007 Wrapup

ASM 2007 ended at noon today. This morning I attended the session dedicated to the International Polar Year (March 2007-March 2008) in relation to microbiology. My favorite talk was by Corien Bakersman and it dealt with the cold adaptation in the psychrophile (no, it doesn't love psychos, they love cold - psychro) Psychrobacter articus. Interestingly enough, instead of identifying amino acid replacements (as in common in such studies), Corien looked for other trends. She discovered that ORFs in P. articus tend to be longer than in mesophiles and she sees that as being explained by selection for encoded proteins to be "floppy" thus preventing them from freezing up in cold temperatures. She also noticed the cell walls of P. articus tend to be less rigid than in mesophiles.

Pictured is Honest Ed's, a classic independent discount store (and Toronto landmark) that started back in 1948 by Ed Mirvish (who is still around, but 91 years old).

Highlights of ASM 2007 -- May 23 and May 24

On Wednesday, I attended two sessions -- one on adaptive landscapes in the morning and another on integrating ecology and evolution into the teaching of microbiology in the afternoon.

The highlight of the morning session was probably the talk by Paul Turner on the effect of co-infection on fitness variance in bacteriophage ϕ6 (which infects Pseudomonas). I hadn't heard about ϕ6 prior to this talk, but it is really quite interesting because much like the influenza virus, it is an RNA virus with multiple segments. When two or more ϕ6 phages infect the same cell, the progeny viruses can have a mixture of segments derived from different "parents". In theory, co-infection could act as a crutch for less fit viruses, as some of their (partial) progeny could be of higher fitness. Turner and colleagues showed that this indeed what happens An earlier version of the work he presented was written up in an article in PLoS Biology.

You might legitimately ask why I attended the afternoon session on integrating ecology and evolution into teaching microbiology (as I don't teach), but maybe I was just drawn to the name of Jo Handelsman, who is rightly renowned for both her teaching and her active research program. Jo is into metagenomics and microbial biodiversity these days, and she talked about how to explain the use of sampling to estimate diversity to undergraduates. She believes that it is easier to start out with concrete simple examples. One of her techniques is to use bags of candies that have different distributions of colors to show that one can underestimate diversity in populations with a majority species (If one draws out three candies and they are all green, one may be tempted to assume that all of the candies are green, perhaps incorrectly).

Thursday morning I had to attend my poster on positive selection in Geobacter. Most people stopping by were more interested in learning how to use PAML in their own systems than in the results, but that was okay as my results are fairly preliminary anyway.

In the afternoon, I attended a session on predation of bacteria. I've long been interested in predators of bacteria (particularly bacterial predators of bacteria such as Bdellovibrio). These days there is quite a battle going on over which of the three main predators (phage, protists, and bacterial predators) is the most important in regulation of bacterial populations in nature. Henry Williams (with whom last year I wrote a grant proposal to sequence environmental isolates of Bdellovibrio-like organisms, unfortunately not funded) gave an interesting talk on comparing the effects of phage versus Bdellovibrio-like predation. He came up with the conclusion that Bdellovibrio and friends are more important because their titers after controlled predation go up several orders of magnitude more than do phage, and this he explained as a result of Bdellovibrio being motile and phages not.

Wednesday, May 23, 2007

Mini-Blogger convention at ASM 2007

I promise I'll write something up on Wednesday's talks, but that would require too much thinking and it's getting late here. Instead, I'll just show this picture demonstrating that I've finally joined the cool blogging world for real. Larry Moran organized a dinner for bloggers attending ASM and invited me as well as other (mostly more established) bloggers. Pictured are (L to R), Larry Moran (Sandwalk), Mona (Science Notes), Andrew Staroscik (Mixotrophy), John Logsdon (Sex, genes and evolution), and Tara Smith (Aetiology). Not pictured are Eva (Eastern Blot) and Chris Condayan, the ASM public outreach manager who later interviewed and filmed us for a feature on science blogging. For some reason (either out of creativity or alcohol consumption) Chris filmed me while having me stand in a phone booth. He's going to edit the interviews into something short and interesting and I'll post a link when it is available (assuming it isn't too embarrassing).

Tuesday, May 22, 2007

Highlights of ASM 2007 -- May 22

There were many shorter (30 min) talks today, so I'll focus on a few that I found most interesting. Janet Siefert gave a interesting talk on her studies of the "living stomatolites" (large cyanobacterial colonies) of the Mexican desert and how they and associated organisms live under such phosphorous-limiting conditions. Particularly interesting was her discovery of a new species of Bacillus that had many apparent cyanobacterial-derived genes. Janet was replacing Ken Nealson (who couldn't attend for health reasons). I had been hoping to meet Ken as one of the many hats he wears is head of the environmental microbiology division of the JCVI, meaning that he's technically been my boss since mid April. Oh well.

Susan Glasauer
talked about her work in studying the biodiversity of metal-reducing bacteria in the Jura mountains of Switzerland. There's more growing there than wine grapes (although the same iron-rich soil that makes for such good wine country is also partly responsible for the microbial diversity)

And to finish off the day, the father of bacterial and archaeal (no, I won't say the "p" word) biodiversity studies, Norm Pace himself, gave an special award lecture as he had been chosen for this year's Abbot-ASM Lifetime Achievement Award. While he made his usual arguments against the use of the word "prokaryote" (which I fully agree with in theory, if not entirely in practice), I found it interesting that he now considers the rRNA tree to represent the nuclear lineage (shades of Jim Lake) rather than the organismal tree.

Highlights of ASM 2007 -- May 21

Monday's talks were all by well-known speakers and were pretty much overviews of topics rather than presentations of any new findings.

Gerry Wright gave an interesting talk on antibiotic resistance. He brought up the points that 1) according to molecular evolution half of all known antibiotics predate the Cambrian explosion and 2) environmental isolates that have never seen a clinical antibiotic quite often have genes for resistance. To understand the development of resistance, we have to stop thinking that the world revolves around humans; we've really stepped into a war between microbes that's been going on long before humans existed.

Ed Delong (one of my heroes) talked about the importance of oxygen-producing bacteria in the oceans and how people tend to forget about their existence and importance, despite these "prokaryotic forests of the sea" producing 50% of the atmospheric oxygen.

And E.O. Wilson (of ants and sociobiology fame) gave a keynote lecture on biodiversity, probably on the basis of his quip made some years ago that if he were a young scientist today, he would become a microbial ecologist rather than an entomologist. It was interesting to hear him talk, as I've heard his rivals Gould and Lewontin speak before, but clearly Wilson's talk was simply a recycled biodiversity of animals talk with a few slides about microbes added -- although I rather liked the (to the general public anyway) more famous Wilson talking about the importance of the work of Woese.

Pictured is the main hall of Union Station -- Toronto's version of New York's Grand Central Station.

Sunday, May 20, 2007

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.

Wednesday, May 16, 2007

Erdös numbers & other geekery

RPM over at Evolgen has recently posted on the (perhaps facetious) need for a version of an Erdös number in biology. If you don't know what an Erdös number is, it basically is the geekier version of "six degrees of Kevin Bacon". Paul Erdös (1913-1996) was a prolific mathematician who had many co-authors. If you co-authored a paper with Erdös, you have an Erdös number of 1, if you didn't collaborate with Erdös himself but instead with one of his collaborators, you have an Erdös number of 2, and so forth. It's a point of pride among mathematicians to have a low Erdös number.

Well, shouldn't biologists join in on the fun? RPM has suggested that Richard Gibbs should be our Erdös. Of course, he's honest enough to mention that he has a Gibbs number of one, but Gibbs isn't actually a bad choice, at least in genomics. I suggested Craig Venter or Claire Fraser (as I have a both a Venter and a Fraser number of 1), but RPM suggested that I wasn't really getting into the spirit of things. Still, (as you'll see), these connections still help me.

So first of all, having done a postdoc in a Computer Science department, I'd just like to state that I have a respectable Erdös number of 4. (Paul Erdös -> Charles Colbourn -> Derek Corneil -> Paul Kearney -> me).

My Gibbs number isn't so bad either, at 2. (Richard Gibbs -> Craig Venter -> me)

Someone on evolgen suggested Eric Lander. My Lander number is 3 (Eric Lander -> Michael Eisen -> Steven Salzberg -> me).

Saturday, May 12, 2007

JCVI Evolutionary Genomics Journal Club on Liu-Ochman

This week I was the presenter for our "Evolutionary Genomics" journal club at JCVI and I chose to present the Liu-Ochman paper on the the stepwise formation of the bacterial flagellum and its reception (part two, three) in the blogosphere. The basic claim of the article is that the 24 core proteins are homologous to each other and this explains how the flagellum evolved through repeated gene duplication events.

Nick Matzke doesn't buy the argument for several reasons: 1) It doesn't seem to be congruent with previous studies 2) At least two of the structures of the presumed homologous proteins don't "look" homologous. and 3) The authors seem to be using the Bl2Seq tool incorrectly. It's odd that Nick focuses so much effort on points 1) and 2) because it is really 3) that is the issue. Personally, I've never been convinced that protein structure is of much use in inferring homology or the lack of it; systematists have been burned so many times by incorrectly assumed (non)homology of gross morphological traits in light of convergent and divergent evolution; why should morphology at the protein level be any different? The beauty of molecular systematics is that it's freed us from having to deal with morphology at all.

At the journal club, we were split on the value of structure for inferring homology, but we all agreed that eyeballing structures, particularly structures that seem to have drawn with different programs and rotated differently. was not a very convincing argument.

We were much more convinced, however, by Nick's demonstration that the authors seem to have performed their BLAST matches incorrectly. As Nick showed, the authors did not have sequence filters enabled, which means that matches to low-complexity regions can artificially inflate BLAST significance, and perhaps more damning, the authors used multiple pairwise BL2Seq runs without correcting for the true size of the search space. And these weren't just assumed to be the problem; Nick demonstrated on a subset of the data that using the correct parameters caused several "significant" BLAST matches to disappear.

This was the introduction to scientific blogging for many of the attendees of the journal club, and they also had some interesting comments about the phenomenon after preparing for the club.

1) While the paper was much mentioned in scientific blogs, generally the mentions were just "Nick Matzke has shown that the Liu-Ochman paper is flawed; here's the link", and not independent analyses of the paper. Yes, this is true of blogs in general, not just scientific ones. But this sort of laziness is very common in traditional media too. Take a look at your newspaper and see how many articles are from news services like AP or Reuters rather than being independent reporting.

2) Why did discussion suddenly fall off after Nick's articles? Does the blogosphere really have such a short attention span?

3) Why haven't we seen a response from Liu and Ochman? Are they not aware of the discussion, or do they simply see criticism on blogs as not being worth responding to?