Thursday, October 28, 2010

The Story behind the Meeting: Lake Arrowhead Microbial Genomes 2010 #LAMG10

Well, I really wanted to write up some thoughtful piece about the Lake Arrowhead Microbial Genomes Meeting I just got back from.  But I am in the throes of prepping for beginning teaching a 700+ person class here at UC Davis and well, I just can't put enough effort into the meeting write up as I would like.  So perhaps my live blog page may be all that I will post directly about the meeting (and at the bottom of this post I am re-posting my feed from Friendfeed).

And if you want to see my slides here they are

And here is a little write up of sorts - more about the history of the meeting than this 2010 meeting.....

First, some background.  The Lake Arrowhead Microbial Genomes meeting was, well, in Lake Arrowhead California.  This is both a town and a lake and is in the San Bernadino Mountains East of Los Angeles.

Fortunately for all of us who were there, UCLA has a conference center in Lake Arrowhead, just off the lake itself.  And for the last at least 12 years, every two years, there is a meeting in September at this Conference Center that focuses on microbial genomes in one way or another.  The meeting has changed names, and has gone through a few different major financial supporters, but has always been organized in a large part by Jeffrey H. Miller from UCLA.  Do not confuse him, please, with Jeffrey F. Miller, another microbiologist from UCLA.  That would be a bad thing.  Sort of like confusing me with my brother Michael.

Anyway, Jeffrey H. Miller has been the major force behind organizing this meeting and he has always done a bang up job on fostering a great atmosphere for both science and interaction.  I am not sure what it is he does, but it always seems to work.  One component is that Miller clearly believe that a conference is not only about hearing talks.  Too many times recently I have been to meetings that were overscheduled with speakers and no time for relaxation or discussion or other activities (the Open Science Summit in Berkeley comes to mind - at that meeting I had to actually stage a coup of sorts to prevent the organizers from skipping lunch and all breaks just to have more talks).  At the Arrowhead meetings, Miller always leaves a few hours in the afternoons free and then has poster viewing/reception time before dinner, plus reception time after evening talks.  It works out well.

The Lake Arrowhead Microbial Genomes meeting has a bit of an unusual history.  It is in essence part of a yearly meeting that used to be go by the name "Small genomes." And every two years, it happens in Lake Arrowhead under the direction of Jeffrey H. Miller.  And since 1998 I have gone to this meeting each time it has come around: 1998, 2000, 2002, 2004, 2006, 2008, and now 2010.

It all started for me in 1998.  I originally signed up for the meeting to give a joint talk with A. John Clark.  I was finishing up my PhD at Stanford on Evolution of DNA Repair Genes, Proteins and Processes and had a post doc lined up to work with Clark at Berkeley.  John was the person who had discovered the recA gene many years before with his graduate student Ann Murgulies. Clark, Steven Sandler and others had been working on functional studies of archaeal homologs of recA and has recently turned their attention in collaboration with Norm Pace (who was then at Berkeley) to trying to use PCR amplification of the archaeal recA homologs to study uncultured archaea, much like Pace and others had done with rRNA. This was seemingly perfect for me as I had worked on both rRNA PCR of uncultured microbes and on evolution of recA (e.g., see here, here, and here) and on DNA repair in archaea.

Anyway, John was invited to give a talk at the Lake Arrowhead meeting and he asked if I would do a tag team talk with him where I could present the results of my phylogenomic analysis of DNA repair genes across the available genome sequences.  So I said sure.  I had no idea what I was getting into, but I went to the meeting.

Alas, there was some awkwardness there because after accepting the post-doc at Berkeley with Clark, I told him I was going to have to drop it.  That was because in the meantime I had finagled my way into going to a dinner with Craig Venter when he came to Stanford to give a talk.  At the dinner I proceeded to tell Craig that I thought some of the evolution stuff he was doing was sketchy and that the genome annotation at TIGR could be improved by phylogenetic analysis.  I drew on napkins, told him about some of my recent papers and eventually he invited me to interview for a job.  The interview went well and both I and my then fiancĂ© now wife were both offered faculty jobs at Craig's institute "TIGR", which we accepted.

So here I was giving a joint talk with Clark yet had just told him I was ditching him for another job.  Well, we soldiered through - but the rest of the meeting went well.  I met all sorts of interesting people, developed multiple collaborations, and had a very good time.  Shortly thereafter I moved to TIGR and began life as a genome sequencer.  For more on the 1998 meeting, alas, there is not much out there on the web.  But I did find my meeting book and some notes and I scanned them in (see below).

So when I got an email in February 2000 inviting me to give a full talk at the 2000 Arrowhead meeting, I accepted immediately.  The 2000 meeting was good and so when I was again invited to talk in 2002 I said yes too.  And so it went.  Back in 2004.  And again in 2006. And again in 2008.  And now again in 2010.  If you want to learn about these past meetings, one way is to go to the meeting web pages.  Those from 2008 and 2006 and 2004 are still up.  Those from prior years are not, but I found two of them by going to the wonderful Internet Archive/Wayback Machine by entering the web address from the other years and changing the year in the http.  See 2002, 2000.  Still trying to track down the 1998 one.

But of course, meeting outlines on the web are not ideal for learning about past meetings.  I have scanned the programs for all the meetings as well as some of my notes, but those too are less than ideal.  I have been unable to find much of interest out there about the meetings before 2006.  But I did blog that 2006 meeting (see here) as well as the one in 2008 (see here and here) where some detail can be found.

It would take too much out of me to retroblog all these past meetings so I am just going to post links to the programs for the ones in 1998, 2000, 2002, 2006, and 2008 (still working on 2004).  I scanned these in, did OCR and converted to PDF.

But I note, perhaps my favorite part of these meetings have been the quotes. Many of these are in the slides from my talk embedded above but here goes

  • Space-time continuum of genes and genomes
  • Gene sequences are the wormhole that allows one to tunnel into the past
  • The human mind can conceive of things with no basis in physical reality
  • Thoughts can go faster than the speed of light
  • The human guts are a real milieu of stuff
  • You better kiss everybody
  • Microbes not only have a lot of sex, they have a lot of weird sex
  • This is how you do metagenomics on 50 dollars, and that’s Canadian dollars
  • Antibiotics do not kill things, they corrupt them
  • There comes a point in life when you have to bring chemists into the picture
  • The rectal swabs are here in tan color
  • And there's Jeffrey Dahmer
  • We are the environment. We live the phenotype.
  • If I have time I will tell you about a dream
  • A paper came out next year
  • We have been using this word for many years without actually realizing it was correct
  • Another thing you need to know" pause "Actually you don't NEED to know any of this
  • "I have been influenced by Fisher Price throughout my life
  • Don't take that away from us
  • It takes 1000 nanobiologists to make one microbiologist
  • I am going to wrap up as I hear the crickets chirping
  • And we will bring out the unused cheese from yesterday
  • In an engineering sense, the vagina is a simple plug flow reactor
  • This is going to be ironic coming from someone who studies circumcision
  • A little bit about time, but I am going to spend a lot less time on time than on space
And with those I will close out my month - delayed posting about the Lake Arrowhead Microbial Genomes Meetings.  Looking forward to 2012.

Here are my tweets as captured by Friendfeed - click on the "View on Friendfeed" button to see the older ones.

Update 9/2012 - Friendfeed embed broken so deleted it.  But some other ways to see some of the notes


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