Social Biology of Microbes 2012 #SocialMicrobes12 wrapup via Storify

Just got back from a meeting on the "Social Biology of Microbes". Here are some notes from my trip and from the talks at the meeting, done via Storify. Here it is as a slideshow:

And here it is a a full scrollable presentation

Social Biology of Microbial Communities

Off to DC for a meeting on the "Social Biology of Microbial Communities" and I thought people out there might like to see the schedule.  Going to try to live blog/tweet so stay tuned ...

Notes from my trip to #AAASMtg #EarthMicrobiomeProject #Storify

I am hoping to write up some more notes from my trip to the AAAS meeting in Vancouver. But for now these pics and this Storification of tweets and related posts will have to do ...

Slideshow version of Storification

w/o a doubt the best aspect of #AAASmtg - giving my kids science schwag #GoScience

Dear #AAAS, I am NOT embargoing my own talk & I plan to record it and post afterwards #embargowatch

Just got another email from AAAS regarding their big meeting in February in Vancouver where I am scheduled to talk:

----------------------------------------
This request for materials is from the AAAS media relations team and is separate from any you may receive from your symposium organizer or the AAAS Annual Meeting office.
----------------------------------------
Dear AAAS Annual Meeting Participant:


Thanks to all of you who uploaded materials to the AAAS Virtual Newsroom by Jan. 16. For those of you who have not submitted materials or want to submit additional materials, you may do so right up through the meeting. The materials will be available online to reporters, although we can no longer guarantee that we'll be able to copy new
submissions at our expense for placement in the on-site library of speaker materials. We will try to include materials received in the next several days in our copy order, however.



You also can make printed copies (10-15 copies) yourself and ship them to Vancouver so that we can place them in the on-site papers library for reporters. Ideally, press materials should be on-site prior to your presentation. Please see below for appended mailing instructions.


Speakers and organizers can submit materials by going to:
http://www.eurekalert.org/aaasnewsroom/mcm/speakers


Your individual username and password for the site:


Please provide the following:


-- A one-paragraph biographical sketch (not a C.V.)


-- A short lay-language summary of your talk, beyond the abstract.


-- The text of your talk, if available, or a related (ideally recent) technical paper, either as a Word file or a PDF. PowerPoint presentations are acceptable, but a full text will better serve reporters' needs.


-- Any additional supporting materials, including multimedia files such as JPEG or TIFF photos in high resolution (300 dpi) and/or digitized video clips.


IMPORTANT: Please note that all AAAS meeting presentations are strictly embargoed and your speaker materials should not be released publicly until the time of your presentation.


If you upload your materials by 16 January, we will copy them at our expense for placement in the on-site library of speaker materials, available only to newsroom registrants.


Please notify your institution's press office of your AAAS Annual Meeting presentation as soon as possible. Your press office can help you submit speaker materials to us and can begin to generate media interest.
....

The thing is - I did not agree to "Embargo" my talk and as I wrote about before, I do not even know what that means.  I figured, in the interest of being "open" about my feelings about this, I should write to AAAS to let them know I was not going to embargo my own talk, and I plan to record my talk and post it afterwards:

To whom it may concern


I am scheduled to speak at the AAAS meeting and I am writing this in regard to the email attached below.  I do not support the notion of an Embargo for my talk and I am unwilling to participate in the embargo. I plan to post information about my talk to the web and to my blog and am writing to specifically let you know I fundamentally do not support the embargo nor did I agree to it when I agreed to give a talk at AAAS.


I also plan to record my own talk and to post the recording and the slides to various websites.  I am not sure if AAAS has a policy about that but wanted to let you know of my plans in the interest of not having any surprises.


Sincerely


Jonathan Eisen

Will report back if I get a reply ... and maybe I can get Ivan Oransky to help make sense out of what a talk embargo means.

AAAS meeting - is this one for embargo watch?

Giving a talk at the AAAS meeting in February in Vancouver.  I have avoided AAAS meetings previously because I do not like AAAS's position on open access issues.  Given that AAAS is at least indirectly a supporter of the recent Research Works Act I am pondering whether or not I will boycott the meeting.   While I ponder that -- I thought I would share the presenter instructions I just got from AAAS (see below).

Apparently, my talk is "embargoed" - though I am not sure I understand how that works for a talk (see the part I highlighted in yellow which, well, I almost certainly will not be following).  I do not understand actually what a talk embargo means - am I supposed to not share with people what I am working on so that every piece of data I present at the meeting will never have ben seen by anyone?  Or am I just not supposed to show my talk to anyone?  What exactly is a talk embargo?  And what will they do when I do not follow it?  Maybe Ivan Oransky knows.



I note - I am surprised AAAS does not try to require me to sign over rights to my presentation to them ...

This request for materials is from the AAAS media relations team and is separate from any you may receive from your symposium organizer or the AAAS Annual Meeting office.

----------------------------------------

Dear AAAS Annual Meeting Participant:

If you have already uploaded your materials to the Virtual Newsroom for the 2012 AAAS Annual Meeting in Vancouver, thank you and please disregard the rest of this e-mail.

For those speakers who have not submitted materials, we'd appreciate your prompt attention to this request. We expect a good turnout of reporters at the meeting in February, and we'd like to provide them as much information as possible about your presentation.

Symposium organizers can help as well by uploading relevant papers or overview documents and encouraging your speakers to submit materials. Papers and speaker materials are for use by reporters in preparing stories and are not made available to general registrants at the meeting.

Speakers and organizers can submit materials by going to:
http://www.eurekalert.org/aaasnewsroom/mcm/speakers

Your individual username and password for the site:

Username: xxxx
Password: xxxx

Please provide the following:

-- A one-paragraph biographical sketch (not a C.V.)

-- A short lay-language summary of your talk, beyond the abstract.

-- The text of your talk, if available, or a related (ideally recent) technical paper, either as a Word file or a PDF. PowerPoint presentations are acceptable, but a full text will better serve reporters' needs.

-- Any additional supporting materials, including multimedia files such as JPEG or TIFF photos in high resolution (300 dpi) and/or digitized video clips.

IMPORTANT: Please note that all AAAS meeting presentations are strictly embargoed and your speaker materials should not be released publicly until the time of your presentation.

If you upload your materials by 16 January, we will copy them at our expense for placement in the on-site library of speaker materials, available only to newsroom registrants.

Please notify your institution's press office of your AAAS Annual Meeting presentation as soon as possible. Your press office can help you submit speaker materials to us and can begin to generate media interest.

If you have any questions, please feel free to contact us.

Meeting of interest: 16th Evolutionary Biology Meeting at Marseilles

Just got an email about a meeting of potential interest and thought I would share:

It is my pleasure to announce that registration and abstract submission for the 16th Evolutionary Biology Meeting at Marseilles, September 18-21, 2012, is open. Please visit the web site of the meeting http://sites.univ-provence.fr/evol-cgr where you will find all relevant information. 

The following subjects will be discussed:

• - Evolutionary biology concepts and modelisations for biological annotation;
• - Biodiversity and Systematics;
• - Comparative genomics and post-genomics (at all taxonomic levels);
• - Functional phylogeny;
• - Environment and biological evolution;
• - Origin of Life and exobiology;
• - Non-adaptative versus adaptative evolution;
• - The « minor » phyla: their usefulness in evolutionary biology knowledge;
• - Convergent evolution

Looking forward to your participation.

My twitter notes from the #NASOneHealth meeting via Storify

I am posting here a wrap up of my notes from the National Academy of Sciences Institute of Medicine Forum on Microbial Threats meeting on Improving Food Safety Through One Health I just attended. I made a little "story" via Storify and that is what I am embedding below. More comments to follow I hope but wanted to get this out there.

Art Meets Science at the Keck Center in DC

Some nice science-art on display at the Keck Center where I was for a NAS/IOM meeting today.  Here are some pics.

Meeting of Interest: DOE JGI "Genomics of Energy and Environment" 3/20-22

A meeting of interest: The Annual DOE JGI User Meeting.  Note - open to anyone - not just those funded by DOE.

Topics include

• Synthetic biology & biodesign
• Systems biology/transcriptional networks
• Application of single cell genomics in microbial ecology and bioprospecting
• Genomic analysis of biofuel traits in maize and switchgrass
• Cloud computing as a platform for large scale sequence analysis
• Ocean viruses: towards population genomics, understanding virus-host interactions, and accessing the uncultured
• Omics in the Arctic: Genome-enabled contributions to carbon cycle and biogeochemical research in high-latitude ecosystems
• Ancient DNA

Plus - Carl Zimmer.  Yes, I said Carl Zimmer.  

Submit Ideas and Vote on Ideas for Presentation Topic Ideas for Special Session at the ASM General Meeting in SF 2012

Calling all microbiology fans - The American Society for Microbiology (ASM) is doing something very different for the 2012 General Meeting in San Francisco that might be of interest.  There will be a special session, organized by the Communications Committee (of which I am a member) where everyone/anyone can propose topics and then these get voted on to determine the winners (see Your Topics, Your Votes, Your Choice).

From the web site

Submit your scientific presentation topic for ASM2012 and then vote and comment on your colleagues’ ideas. The people who submit the top 5 entries will receive a travel subsidy of $800 (or $1200 for international submitters) and will present their topics at the General Meeting in San Francisco, on Tuesday, June 19 at 2:30 p.m., PT.

The submission deadline closes Feb. 1, 2012 at noon, GMT. The top 5 voted topics will then be approved by March 1, 2012.

The rules of the system are as follows (also from the web site)

• All scientists are encouraged to submit, especially undergraduates, graduate students, post-docs and technical staff.
• Registered site users get 10 votes to allocate among topics, with a maximum of 3 votes per topic. However, votes can be reallocated up to the Feb. 1, 2012 deadline.
• Topics must be submitted with a title. A 3 to 5 sentence description is strongly encouraged. You may also include links to additional or background materials by inserting an http:// before a URL in the description field.
• While multiple topics may be submitted. Only one topic per submitter will be selected. In other words, if a submitter gets 3 topics in the top 5 by Feb. 1, 2012, that person will only be allowed to present on one topic at the meeting.
• The submitter must be the presenter.
• No pseudoscience allowed. If you see an entry that looks suspicious, please flag the idea as inappropriate at the end of the topic's description. ASM reserves the right to remove improper submissions and comments.
• Topics must be presented within a 30 minute time slot, 10 minutes of which will be allotted for questions and answers.
• Speakers for invited sessions at ASM2012 are not eligible to participate in this session.

So - please consider submitting ideas and voting on ideas and spreading the word.

Earth Microbiome Project session at AAAS in Vancouver 2/18

This should be fun - session at AAAS meeting in Vancouver.

The Earth Microbiome Project: Modeling the Microbial Planet

Saturday, 18 February 8:30AM-11:30AM

Organized by: Jack A. Gilbert, Argonne National Laboratory, IL

Speakers:

• Folker Meyer, Argonne National Laboratory, IL 
• Developing the Metagenome Data Exchange Format
• Jonathan Eisen, University of California, Davis
• Toward a Field Guide to the Microbes
• Rob Knight, University of Colorado, Boulder
• Uncovering Novel Bioiformatic Techniques for Exploring Microbial Life
• Rick Stevens, Argonne National Laboratory, IL
• High-Performance Computing and Modeling the Microbial World

Fun at #compass11 - or - well - not at the meeting

See the full gallery on Posterous

p227.mov Watch on Posterous

-

Having fun at banking session at #compass11

p186.mov Watch on Posterous

See the full gallery on Posterous

Blast from the past: video of a talk I gave in 2006 #metagenomics

Just re-found this video and posted it to youtube.  It is from a talk I gave in 2006 at the first "International Metagenomics Meeting" in 2006.

I think one may still be able to view videos from the CalIT2/UCSD page here. But I thought it might be better to have this talk on YouTube than at the CalIT site so I posted it ... hope they don't sue me.

Note - I wrote a blog post about the meeting here:
The Tree of Life: Metagenomics 2006

Notes from a trip to Woods Hole, MA to teach #genomics at the MBL Microbial Diversity Course

Here are some notes from my recent trip to Woods Hole, MA where I went to give a talk for the Marine Biological Lab "Microbial Diversity Course".

Day 1:  Thursday

My trip started quite poorly.  I wrote a whole post on the first day so if you want more detail go here: A squatter's journey to the Marine Biological Lab (MBL).  I posted (of course) to twitter along the way.  Here are some of my posts:

• Heading to Woods Hole/MBL-giving talk for symposium for the Microbial Diversity Class http://t.co/o2hx0tf #fb
• Anyone out there recommend best way to get from Logon to Woods Hole after 10:30 PM (no Peter Pan bus) w/o renting car? 
• Got lots of responses to this including from @ctitusbrown and @PhoebeFossil and @larry_parnell
• Best suggestion was from Julie Huber
• Thank you Delta for out early arrival in MSP- not so many thanks for sitting on runway for 20 minutes ad more waiting for gate
• Yhgtbfkm - we finally got to a gate at MSP and the gate agents keep missing our door with jetway
• @nwheat maybe I'll see you as I head to my connection
• Had a long twitter conversation with her about the fact that both of our flights were becoming disasters
• Plane was very late bit now in a nice Prius from Green Shuttles on way to Woods Hole #gomicrobes http://t.co/zwAHWy
• UGGGH - arrived Woods Hole/MBL; got dorm room key at 1am; woman in room not very happy; finally got other hot crummy dorm room; Ahh MBL

Day 2: Friday: Hanging out at MBL

Woke up at the Swope Dorms and, thanks to the lovely reception I got from the Housing Staff (see A squatter's journey to the Marine Biological Lab (MBL) again for more detail) I was not very happy.  I went in to town to get a latte and something to eat and then made it over to the Microbial Diversity Course to hear a few talks and see some of the folks there.  Then I went back to my dorm room, packed up my stuff and abandoned Swope and went to the Sleepy Hollow Motor Inn just up the road, a bit out of town.  I had already called and they held a room for me (I tried the one place actually in town but they were full).  So I checked in, dumped my stuff and then walked back in to town.  I eventually ended up going to dinner with some of the course TAs and other personnel.

Here are some tweets from the day

• Fun- MBL housing team can give me wrong keys for 1 AM checkin but rushes in to new room in early AM b/c I'm a squatter - Ahh MBL
• At least the view is nice #MBL #WoodsHole http://t.co/MPEBmHk
• The Tree of Life: A squatter's journal to the Marine Biological Lab (#MBL) http://goo.gl/fb/yFfXe #travel #teaching

Alas, was quite a bit tired from the horrible trip and bad housing experience so did not tweet much the whole day.  Here are some pics from the day:

View from my second room at Swope

View from my room of Eel Pond

View from my room - nice view - but room was unbearably hot even on a cool day.

Microbial Diversity course lab

Microbial Diversity course lab

Microbial Diversity course lab

Microbial Diversity course lab

Microbial Diversity course lab

Eel Pond again

Eel Pond again

The Kidd

Art around MBL

Art around MBL

Art around MBL

Fun chairs in the Candle House

Fun chairs in the Candle House

Squid on a fence

Squid on a fence

More eel pond

Magical berries

Microbial mat

Microbial mat

Magical berries

Magical berries

Magical berries

Microbial mat

Skate babies

Day 3: Symposium

Saturday was the day for the genomics symposium I had come for.  The symposium was hosted by the Microbial Diversity Course and was focused on microbial genomics.  There were four speakers - me, Howard Ochman, Nancy Moran and Eugene Koonin.  I thought the symposium went quite well --- each speaker did a good job of not both complimenting and complementing the other speakers.   I hope the students liked it.

I spent many hours the night before and in the AM working on my talk, trying to fine tune it for the audience.  I grabbed a latte in the morning at a nice Woods Hole place, and eventually walked on over towards the lab.

• Good morning Woods Hole http://t.co/yyoKrC2 http://t.co/oxGL0aOhttp://t.co/18j6qTh http://t.co/jbUFTaJ

I headed over to Swope and fortunately found a person from the course who told me where the talks were.  I gabbed some breakfast in the dining hall and then went to the room next door where the Symposium was going to be held.  I set up my laptop and alas noticed I had forgotten my Apple remote.  So I did a App store search to see if my iPhone could serve as a remote for Keynote and it can (for 99 cents).  So I downloaded the App and got it working and was ready to go.
I got a nice introduction from Dan Buckley, one of the Course organizers and then gave my talk.  I think I went a bit fast in parts but people seemed to like it.  I got some good questions and then it was time for a break.  Anyway - here are my slides, which I posted on Slideshare: Eisen Talk for MBL Microbial Diversity Course
View more presentations from Jonathan Eisen Then Howard Ochman gave a talk.  Here are some tweets from his talk:

• Done with my talk at MBL for the Microbial Diversity course Symposium on Microbial Genomics - now listening to Howard Ochman
• Howard Ochman discussing how genes in a bacterial genome w/ atypical composition are considered likely to have entered by lateral transfer
• Ochman referencing classic paper by Sueoka "ON THE GENETIC BASIS OF VARIATION & HETEROGENEITY OF DNA BASE COMPOSITION" http://t.co/zBCPHnb
• Ochman showing time course of the plot of genome size vs. # of genes for bacteria - all looked good 1kb=1 gene until M. leprae genome
• Ochman quotes "Less than half of the genome contains functional genes but pseudogenes .... abound" http://t.co/B1SsFd2
• Ochman: Why aren't there lots of pseudogenes in most bacterial genomes? B/c there is a mutation bias towards deletionshttp://t.co/MPZWVHl
• Ochman referencing "Bacterial genome size reduction by experimental evolution" http://t.co/I8jjKLl re: deletion bias
• Ochman making genetic drift personal: sometimes you pull out just the blue M&Ms, which of course you really don't like #funny
• Ochman referencing "The consequences of genetic drift for bacterial genome complexity" http://t.co/hTTatjV
• Ochman: an increase in genetic drift from reduced effective population size can lead to increase in Ka/Ks
• Ochman discussing how effect of drift on bacterial genome size is opposite trend predicted in Lynch and Conery 2003

Then there was a little break for Lunch.  After lunch I had an entertaining conversation with Howard Ochman about various topics.  And then we were back to talks.


Nancy Moran.  Here are my tweets:

• Listening to talk by Nancy Moran about tiny bacterial genomes - she is discussing her work w/ now retired #UCDavis prof. Paul Baumann #fb
• Moran - discussing work of Allison Hansen in her lab on bacterial gene expression in bacteria containing cells in aphid gut
• Moran discussing incredible diversity of insect symbionts that help hosts obtain nutrients from nutrient poor diets #microbesrule
• Moran discussing the Tremblaya genome which has recently shown up in Genbank http://t.co/Cy9ydrz
• GavinHThomas: @phylogenomics Tremblaya is awesome. John McCutchoen is the man - hope this is published soon.
• GavinHThomas: @phylogenomics 58% GC in an insect symbiont - simply weird. McCutcheon talked about this at SGM Insect Symbiosis in Harrogate, UK in April.
• @GavinHThomas yes, high GC but it is related to organisms with even higher GC

Then Eugene Koonin. Here are my tweets from his talk:

• Now listening to the one and only Eugene Koonin discussing evolution of archaea/bacteria at MBL Microbial Diversity course #fb
• I note my start in genome evolution really came from reading papers by Koonin on helicases
• Koonin showing figures from one of my favorite papers of his: ... the emerging dynamic view of the prokaryotic world http://t.co/sHxjYjg
• Koonin: Archaeal genomes are even more gene dense than bacterial genomes
• Koonin: the majority of genes in bacterial and Archaeal genomes are part of conserved families
• Koonin: most gene families show patchy phyletic patterns across bacterial and Archaeal genomes
• Note - Koonin has more than 500 papers listed in Pubmedhttp://t.co/KuU7Oaz
• Koonin : most of the universal genes in bacteria and archaea are involved in translation
• Koonin describes "bureaucratic ceiling" to genome size b/c of exponential incr. in regulators vs. genome size - can't get too big
• TRyanGregory @phylogenomics Limit on "genome size". He means gene number (which does correlate in bact/arch but not euk)
• @TRyanGregory Sorry .. He is only discussing bacteria and archaea ... So here it does correlated w/ genome size
• @TRyanGregory indeed .. He was using gene number as his key feature
• Koonin describing 1998 Aravind et al paper on Aquifex which was 1st report of massive gene transfer between bacteria / archaea
• Side story: when Thermotoga genome paper came out (I was buried as middle author) Koonin called me, POd that we had not refd Aquifex paper
• @leonidkruglyak yes but this was a bit of a big deal ... Press coverage ... Nature paper, etc etc ...
• @leonidkruglyak The funny part was . He was POd at me even though I was buried in the middle b/c he said I should know better ...
• I must say Koonin is giving a damn excellent talk on bacteria and Archaeal evolution
• Koonin discussions how there is a central tree-like structure in the "forest of life" of trees of conserved genes
• Koonin discussions this: Comparison of phylogenetic trees and search for a ... http://t.co/9n9t27Q
• Koonin: there is a strong signal of vertical evolution even among much lateral gene transfer, b/c transfer is mostly random
• ATGC: a DB of orthologous genes from closely related prokaryotic genomes & a research platform for microevolutionhttp://t.co/uAUy5zl
• Koonin: "There is such a thing as a prokaryote" (gives many reasons)
• Koonin discussing my favorite topic these days: CRISPR-CAS system
• Koonin discussing his paper on early finding of crispr elementshttp://t.co/ksp1ZGA
• Prediction: A Nobel in the near future will go for work on CRISPR/CAS system of adaptive immunity in bacteria / archaea
• Koonin discussing the journal he helped start called Biology Directhttp://t.co/2sY75BX which is both #openaccess and has open review
• Koonin has a new Book: The Logic of Chance: The Nature and Origin of Biological Evolution: ProQuest Tech Bookshttp://t.co/94cvGr5

After Koonin was done, everyone dispersed.  I wandered around and took some pics:

Magical mushrooms

Sloan Urinal (inside joke about http://microbe.net

????

I went back to my motel room for a little bit and then headed down to Eel Pond for a Course BBQ.

Deck for party

Deck for party

Photosynth stiched together pic

Eel pond

Party

Party

Party

I then headed in to town where my friend Nipam Patel was having a party for the Embryology Course he was teaching.  And I hung out as his house for a bit and then went back to my room.

Day 4: Home


Got up late.  Checked out.  Wandered into town with my suitcase.  Took some pics.





And after some internal debate, decided to switch my flight to return that day rather than go visit relatives in Boston (sorry Diana, Hal --- just wanted to get home).  So I took the Bonanza Bus to Logan - discovered that Karl Stetter was also going on the bus to Logan.  I tried to watch the US-Brasil women's soccer game on my iPad using the wireless they have on the bus but it was choppy.  So I just followed updates on the game - and even that was exciting.


Here are my tweets from the day:

• I'm at Pie in the Sky (10 Water St, Woods Hole)http://4sq.com/r0HOFh
• MBL -> BOS -> JFK -> SMF - sorry to leave microbial diversity course; wonder if @lancearmstrong will still be in #Davisca tonight 
• Eel pond - Woods Hole, MA - last night #fb twitpic.com/5ob3ka twitpic.com/5ob3iy #fb
• Can't get away from the deepsea - even at Logan Airporthttp://t.co/3k8gX3t
• #Scienceart at MBL in Woods Hole twitpic.com/5oc5f0twitpic.com/5oc5bj twitpic.com/5oc5vd twitpic.com/5oc5fbtwitpic.com/5oc625