Tag Archives: Lake Arrowhead

Lake Arrowhead Microbial Genomes Meeting 2012 Speaker Gender Ratio #LAMG12

Got some questions about the Lake Arrowhead Microbial Genomes 2012 Meeting in regard to gender ratio of speakers and organizers, after I have been complaining about ratio at other meetings.  Here is the full list of speakers and organizers for this meeting.  Women in bold.
Organizers:
  1. Jeffrey H. Miller
  2. Jonathan Eisen
  3. Ashlee Earl
  4. Lisa Raleigh
So the organizers are a 50-50 split.
Speakers (in order)
  1. Jonathan Eisen
  2. Nina R. Salama
  3. Frederic Bushman
  4. Kristine Wylie
  5. Janet K. Jansson
  6. Forrest Rohwer
  7. Curtis Huttenhower
  8. Tanja Woyke
  9. Maomeng Tong
  10. Jeffrey Cox
  11. Susannah Tringe
  12. Julian Parkhill
  13. Rustem F. Ismagilov
  14. Gautam Dantas
  15. Pamela Yeh
  16. Mike Gilmore
  17. Lance B. Price
  18. James Meadow
  19. Jason E. Stajich
  20. Laura Sauder
  21. Tara Schwartz
  22. Susanna Remold
  23. Bernhard Palsson
  24. Anca Segall
  25. Trent Northern
  26. Rick Morgan
  27. Beth Shank
  28. Morgan Langille (added)
  29. Anthony Fodor (added)
  30. Peter Karp
  31. Tatiana Tatusova
  32. Timothy Harkins
  33. Katrine Whiteson
  34. Mallory Embree
  35. Varum Mazumdar
  36. Abigail McGuire
  37. Ee-Been Goh
  38. Shota Atsumi
  39. Howard Xu

So 37 39 speakers, 16 of which are women.  So that comes to 43.2 41%.

Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting

Meeting went well.  Here is a storification of it:

http://storify.com/phylogenomics/lake-arrowhead-microbial-genomes-2012-lamg12.js?template=slideshow[View the story “Lake Arrowhead Microbial Genomes 2012 #LAMG12” on Storify]

History of the Lake Arrowhead Microbial Genomes meetings

Recommended meeting for those interested in microbial diversity and/or microbial genomics: Microbial Genomics – ARROWHEAD 2012

Among the reasons to go:

And if you want to know more about past meetings see below:

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 fiancé 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

2004

  • 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

2006

  • 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

2008

  • 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

2010

  • 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

It’s Miller Time – Lake Arrowhead Microbial Genomes Conference — about to begin

Well, I am back.  Every two years I come back to this small meeting about small genomes.  The meeting is officially the “16th Annual International Meeting on Microbial Genomics at Lake Arrowhead, CA” but in reality, every two years it is at Lake Arrowhead and every other two years it is elsewhere.  And I rarely go to the other one — but I keep coming back to Lake Arrowhead.

Why?  Well, you might guess it is because it is at UCLA’s conference center up in the mountains.  But you would be wrong.  You might guess it is because I generally hate big meetings and this one is nice and small/medium.  But you would be wrong again.  For there are lots of meetings in pretty places.  And there are lots of medium sized meetings an omnivore like me could go to.  I go back every two years because of Jeffrey H. Miller, the organizer.  He invites me.  I can never say no.  
Why? Well, many reasons.  Sure one is that I like him.  Another is that he does meetings in the right way (not too many talks in one day — some time to relax and talk with other people and to interact, etc).  But the truth is, I say yes because he is one of the few people I know who is interested in both DNA repair processes and microbial genomes.  And his meetings reflect this interest.  So I guess even though I do not spend enough time working on DNA repair any more, I did do my PhD on it, and I did basically try and copy some classic Jeffrey Miller mutator experiments.  So I just have to go to this meeting.  And here I am (see my 2006 meeting notes here) – despite having been very sick this summer and getting ready to teach a new class in the fall with 400+ students.
Anyway – More on the meeting coming.Here are the talks for those interested
James C. Liao
University of California, Los Angeles, CA
“Non-fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels”

Jonathan Eisen
University of California, Davis, CA
“A Genomic Encyclopedia of Bacteria and Archaea”

Bernhard Palsson
University of California, San Diego, CA
“The Genetic Basis for Adaptive Evolution in E. coli”

George Weinstock
Baylor College of Medicine, Cambridge, MA
“The Human Microbiome: Progress and Challenges”

Gary Siuzdak
The Scripps Research Institute, La Jolla, CA
“Metabolomics Reveals Large Effect of Gut Microflora on Biochemistry and Activation of a Host Response”

Jim Bristow
DOE Joint Genomme Institute, Walnut Creek, CA
“Microbial Sequencing for Biofuels Applications”

 Eric Wommack
University of Delaware, Newark, DE
“Making sense of the chaff: What will metagenomic approaches tell us about viral ecology?

Valérie de Crécy-Lagard
University of Florida, Gainesville, FL
“Making Sense of Genomes: Linking Gene and Function by Comparative Genomics”

Trent Northen
The Scripps Research Institute, La Jolla, CA
“High Throughput Mass Spectrometry Based Metabolomic and Enzymatic Assays for Functional Genomics”

Matteo Pellegrini
University of California, Los Angeles, CA
“New Methods for Processing High-throughput Sequencing Data: Improving the Solexa/Illumina Data Analysis Pipeline”

Sabeeha S. Merchant
University of California, Los Angeles, CA
“Transcriptomics of Nutritional Copper Homeostasis in Chlamydomonas”

Lynn L. Silver
LL Silver Consulting, LLC, Springfield, NJ
“The State of Antibacterial Discovery in 15 minutes”

Julian Parkhill
Welcome Trust Sanger Institute, Cambridge, UK
“Discovering Variation in Genetically Monomorphic Bacteria: SNPs and the Evolution of Salmonella Typhi”

Tiffany Williams
Baylor College of Medicine, Houston, TX
“Global Health and Next Generation Sequencing Technologies: Streptococcus pneumoniae sertoype 1 in Africa”

Kim Lewis
Northeastern University, Boston, MA
“Persister Cells and Biofilm Resistance”

Jeffery F. Miller
University of California, Los Angeles, CA
“Diversity-Generating Retroelements”

Steven A. Benner
Foundation for Applied Molecular Evolution, Gainesville, FL
“Molecular Paleoscience”

Joe Zhou
University of Oklahoma, Norman, OK
“Metagenomics Insights of the Feedback Responses of a Grassland Ecosystem to Elevated Atmospheric CO2”
Heather Allen
University of Wisconsin-Madison, WI
“Using Functional Metagenomics to Discover Antibiotic Resistance Genes in Natural Environments”

David A. Relman
Stanford University School of Medicine, Stanford, CA
“Response of the Human Distal Gut Mircobiota to Disturbance: The Effect of Antibiotics”

Ashlee Earl
Harvard Medical School, Boston, MA
“Bacillus subtilis Biofilm Diversity”

Mary E. Lidstrom
University of Washington, Seattle, WA
“Coupling Function to Phylogeny via Single-Cell Phenotyping”

John Dueber
University of California, Berkeley, CA
“Use of Synthetic Protein Scaffolds to Balance Pathway Flux of Engineered Metabolic Pathways”

Maria L. Ghirardi
National Renewable Energy Laboratory, Golden, CO
“Hydrogen Fuel Production by Microalgae: Issues and Future Directions“

Caroline S. Harwood
University of Washington, Seattle, WA
“Redirection of Metabolism of Hydrogen Production”

Byung-Kwan Cho
University of California, San Diego, CA
“The Reconstruction of the Transcriptional Regulatory Network in E. coli ”

E. Virginia Armbrust
University of Washington, Seattle, WA
“Molecular Insights into Silicon Bioprocesses in Marine Diatoms”

Athanasios Typas
University of California, San Francisco
“High-throughput Quantitative Analysis of Genetic and Chemical-Genetic Interactions in E. coli”

Devaki Bhaya
Carnegie Institution for Science, Stanford, CA
“Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.”

Erin Sanders-Lorenz
University of California, Los Angeles, CA
“Integrating Discovery-based Undergraduate Research Experiences into UCLA Courses Using a Collaborative Curriculum Model”

Cheryl Kerfeld
DOE Joint Genome Institute, Walnut Creek, CA
“The JGI Microbial Genome Annotation Program”

Fredrick Blattner
University of Wisconsin, Madison, Wisconsin
“Insights from the Genomes of Commonly Used Lab Strains”

Colin J. Ingham
Wageningen University, Wageningen, The Netherlands
“Reinventing the Petri Dish: Miniaturized Tools for High Throughput Microbial Culture”
Maureen Hillenmeyer
Stanford University, Stanford, CA
“The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes”

Simon Prochnik
DOE – Joint Genome Institute, Walnut Creek, CA
“The Genome Sequence of the Deep-Branching Amoeboflagellate Naegleria gruberi Reveals Ancestral Eukarotic Functions”

Elizabeth Fozo
National Institute of Allergy and Infectious Diseases, Bethesda,MD
“Regulating Bacterial Expression of Short Hydrophobic Toxic Proteins with Small RNAs”

Mariusz Nowacki
Princeton University, Princeton, NJ
“RNA-mediated Epigenetic Programming of a Genome-Rearrangement Pathway”

Barry L. Wanner
Purdue University, West Lafayette, IN
“Development of the http://www.EcoliHub.org Information Resource”

Hirotada Mori
Nara Institute of Science and Technology, Nara, Japan
“Systematic Analysis of Genetic Interaction of Esccherichia coli”

Genomics Education highlighted at 14th Annual International Meeting on Microbial Genomics

Just got back from the 14th Annual International Meeting on Microbial Genomics, where I gave talk on microbial symbiont genomics. This was one of the best meetings I have been to in a while. It had the right combination of everything including:

  1. Many excellent talks and posters (OK, in the interest of not upsetting people for not saying their talk or poster was great, I will not make a big list of all the ones I thought were good, but I will give a few highlights below).
  2. Excellent location (UCLAs Lake Arrowhead Conference Center, which is in the mountains east of Los Angeles). This is a place that is very conducive to getting to know colleagues and it almost forces interaction among people. There is one central building where there is a dining hall, a nice deck if you want to eat outside, the conference room, rooms for posters, and a large living room for hanging out. The rooms for sleeping are mostly great (e.g., mine was a split level condo like structure with a living room and a bedroom/bath on floor one and a bedroom/bath on floor 2). And being in the mountains is very pleasant. Plus there is a pool, jacuzzi, and sports facilities that are very nice. The only annoying thing is that the Lake itself, which is 100 yards away, but it really almost private, with most of the shoreline occupied by houses and private docks.
  3. Good food. The food is not spectacular or anything but better than the food at 90% of the conferences I have been at.

In terms of talks, there were quite of few that were both interesting topics and very well presented. For example, Jessica Green from U. C. Merced gave a great talk about spatial distributions of microorganisms, Julian Parkhill from the Sanger Center put together a really nice story about mechanisms by which microbial pathogens generate phenotypic diversity, and Julie Huber from MBL impressed many with her talk about the “Deep Rare Biosphere.”

But to me, the best two talks were ones on science education reform by two people from UCLA. Erin Sanders-Lorenz presented a summary of her course she has been teaching at UCLA that has students doing “phylogenomic” analysis which takes them from isolating and culturing organisms from environmental samples to building evolutionary trees of genes isolated from these cultured species.. This seemed like a very creative, hand on, novel way to teach students the excitement of science and some things about evolution. It sounded so well thought out that I asked for (and got) a copy of her lab manual.

Much as I liked this class, the one described by Cheryl Kerfeld knocked my socks off. She described a program they have developed at UCLA called the Undergraduate Genomics Research Initiative. This is an interdepartmental multi-course collaboration with the central theme involving the sequencing and analysis of the genome of a bacterium called Ammonifex degensii. The various courses are organized around a central course on genome sequencing. The linked courses include ones in many different departments at UCLA as well as various courses at other universities. They have clearly given enormous thought to how to do a truly project based course which likely will catch students attention and interest much more than standard lectures or standard labs.

There have been other successful hands on genome sequencing courses before – perhaps the first being one by Brad Goodner at Hiram College who had students participate in the sequencing and analysis of the genome of Agrobacterium tumefaciens (e.g., see a press release here). The Kerfeld UCLA UGRI program sounds like it has gone to the next level by integrating many courses across departments and by having creative ways to encourage participation of students in multiple aspects of the project. It really is worth giving a look at the UCLA UGRI program’s web site.

Other tidbits about the meeting:

  • Jeffrey H. Miller from UCLA organized it
  • This is the same Jeffrey Miller who identified most of the mutator genes in E. coli with a really creative genetic screen
  • There was another Jeffrey Miller from UCLA at the meeting (will leave this up to google for people to figure out who this other Miller is).