10th Anniversary of my Defense -- A Retrospective

On December 2, 1998 I defended my dissertation entitled "Exploration of microbial genomic sequences via comparative analysis", the somewhat vague title referring to a collection of projects that I worked on in Gary Olsen's (pictured) laboratory at the University of Illinois at Urbana-Champaign, most notably the CRITICA genefinder (which was, until a year or so ago, still in use at JGI), and one of the earliest genomic studies of thermostability.

My thesis committee consisted of Carl Woese, Tony Crofts, and Stan Maloy (now at SDSU; I run into him at seminars occasionally). 

I don't have any pictures of the defense or the lunch afterwords after owning to a sad accident -- my parents' camera had a broken lens, and in that pre-digital era, they didn't know anything was wrong until they tried to develop the film. Still, the day sticks with me in memory. I gave what was probably the best presentation of my career (probably because I had practiced ten times or so), and the questioning was very friendly (the serious questioning had been several years before at my prelim). 

I've worked a number of jobs moving to various cities in the name of science since those days -- a postdoc in Computer Science at the University of Waterloo,  a senior bioinformatics scientist at a now-defunct biotech firm in Montreal,  living in downtown DC while working in the microbial genomics departments of TIGR and its successor JCVI,  and now in San Diego, where I'm working at the west-coast campus of JCVI. Who knows where the next ten years will take me?

Extreme 2008 and Extreme Viruses

A research expedition aboard the famed R/V Atlantis (carrying the equally well known submersible DSV Alvin) has just set sail from Manzanillo, Mexico. Its 21-day mission is to explore hydrothermal vents in the Pacific and Sea of Cortes. That's what the "Extreme" part is -- they aren't going to bungee jump or anything. 

I actually know (although not well) the two PIs who are leading the expedition -- I met Craig Cary in Australia at ISME last summer and I met Eric Wommack in Boston at ASM last spring. However, my principal interest in the expedition is that two of my JCVI co-workers, Lisa Zeigler and Doug Fadrosh, are aboard in order to collect viruses in the vent community. Viral ecology is a growing field -- viruses play a role in microbial ecology both as predators and as means of transferring genes from host to host.

The expedition has a lovely official site, and Lisa has started a blog that all of you should go visit -- blogging/journalling has a long and noble tradition in marine biology expeditions, going back at least as far as Darwin's "Voyage of the Beagle".

Is that a duck? It sure sounds like one!

Only a few days ago, my former TIGR colleague Steve Salzberg wrote about Johns Hopkins University's plans to open an "Integrative Medical Center" where herbalism and other "alternative" (that is, unscientific) treatments will be offered. That was disturbing enough given the great stature Johns Hopkins has in medical science. 

But today I received an e-mail that the East Coast branch of the JCVI, the institute where I work, as part of their "Lunch & Learn" series, is inviting a speaker from the "North Adams Wellness Corner" to talk about

"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."

Not very promising. I'd be far more convinced by peer-reviewed articles rather than the anecdotal experience of Bruce Lee and his predecessors. Why is it that nonsense sounds more profound when it is from China or India? The West also had its pre-scientific medical theories. Why not return to the Four Humours of Hippocrates? This is even older than the "eight brocades", and according to the above logic, older is better, right? I guess the reason why I'm angry about this quackery is that I have too much yellow bile ("choleric").

Badgeromics 2008, er Metagenomics 2008

I'm attending the Metagenomics 2008 conference being held locally at UCSD. There's plenty of interesting talks (see Jonathan Eisen's coverage). However, today what struck me the most (egotist that I am) was how my work was brought up in three separate talks...

Alex Worden started out the day by discussing her work on picoeukaryotes (unicellular eukaryotes less than 2 microns in size) and there were a couple of slides dealing with the comparative work that Andy and I have done as part of her forthcoming Micromonas paper.

Then practically half of Shannon Williamson's talk about her metagenomics work on marine viruses was devoted to my phylogenetic pipeline, APIS (Automated Phylogenetic Inference System), which performs taxonomic binning of metagenomic data by the automated creation and interpretation of phylogenetic trees.

Then in the evening Jonathan Eisen brought up our 2005 paper as part of the justification for his new project to sequence hundreds of bacterial and archaeal genomes.

Thanks guys. Your checks are in the mail...

The Genome Sequence of Phaeodactylum tricornutum

What's this? Another eukaryotic genome paper with me on it? I blame Jonathan Eisen for putting me on that road to ruin -- I never touched the nucleated rascals before Tetrahymena. 

But seriously, single celled eukaryotes are cool, and not Eisen but rather Andy Allen (who doesn't have a web page or blog to link to, unfortunately) is the one to blame for getting me involved with his beloved diatoms.

P. tricornutum is the second diatom genome to be sequenced, and first of the pennate (elongated) lineage. We discovered that this genome was quite different from that of Thalassiosira pseudonana, the first diatom genome to be sequenced , which is a member of the centric (hatbox/cheesebox/petri dish) lineage.  We also identified about 600 genes that we believe to be of bacterial origin in this genome. As this was part of the analysis that I did, I'm perhaps biased in that I think this one of the most interesting results in the paper. This analysis wasn't just "BLASTology" (being just based on BLAST output), but rather based on phylogenetic trees for each predicted protein coding gene in the P. tricornutum genome.

There's been some press about the paper -- including this one in the German newspaper Die Welt -- whose sub heading "Diese Lebewesen entpuppen sich als eine kuriose Mischung aus Pflanze, Tier und Bakterium" implies that P. tricornutum is a curious mix of plant, animal, and bacterium -- not exactly true, but hints at the HGT analysis that we did. There's also this press release that mentions me and Andy by name, but so far no papers have used that part :-) 

Anyway, the paper (which is under a Creative Commons License, showing that even commercial publishers like Nature can be reasonable) is up on Nature's advance publication page as of yesterday. Check it out. And the supplemental, where most of the actual data is.

The Genome Sequence of Penicillium chrysogenum

With all the work I've been doing in metagenomics, it's nice to be reminded that I still do some of the non-meta type -- yes, I was involved in the P. chrysogenum project, and the paper  (and supplemental) is now up in Nature Biotechnology's Advance Publications page prior to the print publication.

We've actually gotten a little bit of press -- the BBC has a brief article here. 

P. chrysogenum is one of those obvious genomes people are surprised to learn haven't been sequenced yet (well until now). While a "pure" biologist may yawn and say "it's just another filamentous fungus -- haven't we sequenced those already?", there is real practical potential for metabolic engineering of new antibiotics from this genome given that researchers have been doing work on the bug for over 60 years. Besides, the genome wasn't completely uninteresting even from the viewpoint of basic science -- we snuck in a fairly controversial fungal phylogeny in figure 2 -- and I stand by it as we used far more data in our alignments than in previous studies.

[updated links to final published version 10/14/08]

RIP David Foster Wallace (1962-2008)

You may have heard the news; last Friday the literary Wunderkind of the 1990s, David Foster Wallace, hanged himself in his Southern Californian home.  I have to admit that I haven't thought much about Wallace since the turn of the century, but his 1996 Infinite Jest was (and perhaps still is) one of my favorite novels.  

In many ways, _Infinite Jest_ was the quintessential 1990s American novel -- the conceit of the story was that American economic and cultural influence would simply keep growing and growing in the future -- as indeed in those heady post-Cold War times it looked like it would.  Of course, part of Wallace's point was that would not necessarily be a good thing given the crass commercialization of US culture  -- his idea that names of calendar years would be sold to the highest bidder is entirely believable given that we live in the world of PETCO Park and Qualcomm Stadium.

Many people have compared Wallace to Bret Easton Ellis (Less than Zero, American Psycho), and in a way they have a point. Certainly, Wallace was far more erudite and literary, but just as Ellis captured the "soul" of Reagan-era America, Wallace did the same for the Clinton era. Who will do the same for our current era?