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Earth Microbiome Session at AAAS 2012

At the AAAS Meeting in Vancouver in February there was a session focusing on “The Earth Microbiome Project” and related topics. The session was organized by Jack Gilbert and had a series of talks that may be of interest to those concerned about the microbiology of the built environment. I gave a talk in the session on “A Field Guide to the Microbes” for which the built environment is a key component.

I will try and post more details about the meeting but for know some may be interested in the “Storification” notes I made based upon twitter posts for the session.  The storification is below.

 

A Field Guide to Bacteria (Comstock Book)
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    At my talk at #AAASMTG I will also discuss phylosift.wordpress.com/ta… plosone.org/article/info%3… and other things
    Sat, Feb 18 2012 12:38:18
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    To those at #AAASmtg, please ensure @phylogenomics at least *mentions* eukaryotes in his talk. Nematodes are (operationally) microbes too!
    Sat, Feb 18 2012 12:37:17
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    Rob Knight at #AAASMtg – of currently available rRNA data Earth Microbiome Project in last year covers >80% of known diversity
    Sat, Feb 18 2012 12:43:17
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    Rob Knight talks of his vision for personalized medicine in developing word by focusing on microbes #AAASMtg
    Sat, Feb 18 2012 12:45:08
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    @phylogenomics I hope you’re telling your microbe-loving friends at #aaasmtg where they can find great microbe artwork etsy.com/shop/artologica
    Sat, Feb 18 2012 12:49:31
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    Don’t forget to support microbial culture : etsy.com/shop/artologica #microbialart #aaasmtg
    Sat, Feb 18 2012 12:52:02
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    Earth Microbiome Project breakfast theatre listening to @gilbertjacka at #AAASMtg http://pic.twitter.com/iDHN93A0
    Sat, Feb 18 2012 13:00:35
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    Have to jump out of the #microbiome talk … follow @phylogenomics @digitalbio @hcpearson @gilbertjacka for the latest from #aaasmtg #emp
    Sat, Feb 18 2012 13:05:37
  • Jack Gilbert Talk
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    Now @gilbertjacka discusses how to model future microbial community change … “microbe weather reports” #aaasmtg #emp
    Sat, Feb 18 2012 12:58:33
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    Microbes see us as “just a new lump of flesh that has come along in the last 2 million years” – @gilbertjacka #emp #aaasmtg
    Sat, Feb 18 2012 13:00:18
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    “The Earth Microbiome Project is saving the lives of babies around the world and must be funded” says @gilbertjacka at #AAASMtg
    Sat, Feb 18 2012 13:05:39
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    #emp is saving babies! @gilbertjacka #aaasmtg
    Sat, Feb 18 2012 13:06:05
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    #mep is saving babies around the world. It must get funded or the babies will die says @gilbertjacka #aaasmtg
    Sat, Feb 18 2012 13:06:05
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    UK native @gilbertjacka shows pic of English Channel and says “This is why I am not considered European” #AAASMtg
    Sat, Feb 18 2012 13:07:16
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    @gilbertjacka gets big laughs for a line about Plymouth Rock and says “That’s it – I’m out of here” and starts walking off stage #AAASMtg
    Sat, Feb 18 2012 13:08:17
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    Jack Gilbert @gilbertjacka continues to do a part science talk part comedy show – now is praising the “hairball” figure style #AAASMtg
    Sat, Feb 18 2012 13:16:44
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    @gilbertjacka: Pilgrims were from south Hampton. Shocking!! #aaasmtg
    Sat, Feb 18 2012 13:07:50
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    “I always like to be shocked” says @gilbertjacka at #AAASMtg
    Sat, Feb 18 2012 13:20:10
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    We don’t have species names for bacteria–we call them OTU1, OTU2, OTU3, OT4…. @gilbertjacka, scientist/comedian #AAASmtg
    Sat, Feb 18 2012 13:14:01
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    Jack Gilbert @gilbertjacka continues to do a part science talk part comedy show – now is praising the “hairball” figure style #AAASMtg
    Sat, Feb 18 2012 13:16:44
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    Can predict species abundance over time/space but wanted to know what they were doing….enter the #Hairball! @gilbertjacka #AAASmtg
    Sat, Feb 18 2012 13:17:07
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    I’m loving the tweets from Earth Microbiome session at #aaasmtg. Thanks @lizabio @b0yle @phylogenomics!
    Sat, Feb 18 2012 13:25:24
  • My talk
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    Don’t keep it secret, don’t follow these notions that we’re not supposed to talk @ things. @phylogenomics on #klllthembargo #AAASmtg
    Sat, Feb 18 2012 13:29:00
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    Me too! Thx! RT: @hillaryrosner: I’m loving the tweets from Earth Microbiome session at #aaasmtg. Thanks @lizabio @b0yle @phylogenomics
    Sat, Feb 18 2012 13:29:42
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    my talk is on slideshare so share it, mock it, blog it, discuss it, comment on it, just don’t keep it secret. –@phylogenomics #aaasmtg #emp
    Sat, Feb 18 2012 13:29:42
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    LOL,will need a recap at GSC Shenzhen MT @phylogenomics: @gilbertjacka does science talk/comedy show, praises “hairball” figures at #AAASMtg
    Sat, Feb 18 2012 13:31:13
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    Birders share when they see an unusual bird & quickly ID’d an Amer. robin in England. Need same tools for #microbes @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:32:08
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    Eisen: Birders saw American robin in Grimsby, UK until it was eaten by local predator. The anomoly quickly noticed & info shared. #AAASmtg
    Sat, Feb 18 2012 13:32:17
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    RT @digitalbio: @phylogenomics is imploring us to publicize his talk as much as possible. Blog , tweet, etc. #AAASmtg
    Sat, Feb 18 2012 13:33:48
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    @phylogenomics wants field guide to microbes like field guide to birds w/ iPhone apps etc. usable by amateurs in powerful ways #aaasmtg #emp
    Sat, Feb 18 2012 13:34:35
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    Preliminary attempts: A Field Guide to Bacteria by Dyer. Anyone interested in #microbes, must get this book. @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:35:36
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    http://www.amazon.com/gp/aw/d/0801488540 – a field gude to Bactria by Dyer – @phylogenomics #awesome #EMP #AAASmtg
    Sat, Feb 18 2012 13:35:40
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    Jonathan Eisen (UC-Davis) says we can’t catalogue microbes with the same thoroughness as birds — but that’s the “drive” of EMP. #AAASmtg
    Sat, Feb 18 2012 13:39:24
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    ~8K described bacterial species, m/b billions of niches–a field guide ludicrous but worthy org principle for study @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:40:16
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    @lizabio What is @phylogenomics calling a bacterial species? #AAASmtg
    Sat, Feb 18 2012 13:40:49
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    ~50 papers studying # of species fo bacteria and #archaea. Lots of complications–like, what is a #species? @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:41:16
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    Need to forget constraints re: how people traditionally think about describing species. @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:43:07
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    You can divide #microbes into species-like categories or instead use branch length, phylogenetic diversity. @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:44:39
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    Matt Kane named me, Rob, Jonathan, Forest, and Janet – Professor Eisen-Man, Jack of All Trades, The Knight, Captain Goth and Stockholm Storm
    Sat, Feb 18 2012 13:44:35
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    @lizabio @phylogenomics Mmm, I was just asking since the previous #AAASmtg mentioned over 8k species found
    Sat, Feb 18 2012 13:47:02
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    This is our planet, we need to characterize microbial diversity on the planet. Even if it seems intractable. @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:47:57
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    We can start to ask if there’s niche characterization in different taxonomic groups of #microbes. @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:49:56
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    Jack Gilbert and Jonathan Eisen give excellent and entertaining perspectives on the importance of understanding the microbial world.
    Sat, Feb 18 2012 13:51:31
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    Awesome: “If you want to grab the data and publish a paper before we do, that’s great” re: 800 seq’d genomes @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:53:11
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    inspired by amateur birders, @phylogenomics held citizen microbiology workshop at UC Davis. #aaasmtg #emp
    Sat, Feb 18 2012 13:56:01
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    Use citizen science to engage amateurs to catalog #microbes like birds. OK, it’s a problem u can’t see them, but… @phylogenomics #AAASmtg
    Sat, Feb 18 2012 13:56:34
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    Eisen calls for more amateur participation in the EMP and citizen microbio. There’s “enormous potential” for popular engagement. #AAASmtg
    Sat, Feb 18 2012 13:56:26
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    @lizabio But we can crowdsource samples at least-think the focus for microbial cit sci will be interpretive tools cc @phylogenomics #AAASmtg
    Sat, Feb 18 2012 14:01:00
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    We’re videotaping interviews at #AAASmtg on why scientists should use social media. @DrBondar @ericmjohnson @JLVernonPhD @phylogenomics?
    Sat, Feb 18 2012 14:03:22
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    Brilliant & entertaining talk on discovering the microbial universe RT@phylogenomics: My slides for #AAASMtg talk slidesha.re/zi7cVP
    Sat, Feb 18 2012 14:04:18
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    Why #microbes hard to culture? Partly b/c org’s have complex interactions, share metabolites, structures, signals @phylogenomics #AAASmtg
    Sat, Feb 18 2012 14:06:50
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    We want full engagement in sci. process for #microbes (not crowdsourcing). Easier for undergrads than public. @phylogenomics #AAASmtg
    Sat, Feb 18 2012 14:21:16
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    @phylogenomics wants us to start pronouncing QIIME “Qweeme” :-) #EMP #AAASmtg
    Sat, Feb 18 2012 14:25:41
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    v amusing story from @phylogenomics at #aaasmtg on bird watchers spotting US robin in UK, then watching it get eaten by bigger bird
    Sat, Feb 18 2012 15:25:36
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    The #AAASmtg #EMP session speakers http://pic.twitter.com/12pXfxmh
    Sat, Feb 18 2012 14:10:01
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    #AAASmtg #EMP great questions from the floor http://pic.twitter.com/3s0Tjzsz
    Sat, Feb 18 2012 14:12:14
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    The EMP crew at #AAASmtg http://pic.twitter.com/jMqP9l4q
    Sat, Feb 18 2012 16:13:40
  • Heather Joseph talk
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    Heather Joseph discussing “ELife” journal – which aims to be great (I love notion of aiming to be great; who would aim to suck?) #AAASmtg
    Sat, Feb 18 2012 17:00:14
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    Heather Joseph discussing open data issues – need to connect data to literature in a better way #AAASMtg
    Sat, Feb 18 2012 17:00:55
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    Heather Joseph pushing the need for Open Education Resources to help translate research material back into teaching #AAASMtg
    Sat, Feb 18 2012 17:01:50
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    Heather Joseph discussing the value and heavy use of Pubmed Central #AAASMtg “No publisher has been harmed in the making of this policy”
    Sat, Feb 18 2012 17:06:08
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    Heather Joseph discussing HR3699 “The numbers I see in my sleep” – the Research Works Act #AAASMtg
    Sat, Feb 18 2012 17:07:36
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    Heather Joseph referencing backlash to the RWA #AAASMtg
    Sat, Feb 18 2012 17:08:25
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    Joseph giving kudos to AAAS for opposing RWA svpow.wordpress.com/2012/0… tho I note; AAAS not doing enough in access phylogenomics.blogspot.com… #AAASMtg
    Sat, Feb 18 2012 17:10:45
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    Joseph: 1) learn more about OA 2) be conscious of where you publish 3) understand that IP should be respected but needs updating #AAASMtg
    Sat, Feb 18 2012 17:12:09
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    Joseph: try to use Creative Commons licenses for your work; talk to scholarly societies, promote a campus wide OA policy #AAASMtg
    Sat, Feb 18 2012 17:13:08
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    Joseph: consider joining Alliance for Taxpayer Access taxpayeraccess.org/ #AAASMtg
    Sat, Feb 18 2012 17:14:03
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    agree! RT: @phylogenomics: Heather Joseph pushing need for Open Education Resources to help translate research back into teaching #AAASMtg
    Sat, Feb 18 2012 18:20:23
  • Lunch
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    Overheard at lunch – for the last year I’ve done nothing but boing boing and book #AAASmtg
    Sat, Feb 18 2012 18:20:41
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    Discussing science faux pas at the tweetup at #aaasmtg phylogenomics.blogspot.com…
    Sun, Feb 19 2012 01:11:27
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    RT @tysune: Collaborative notes for “Moving (Actively) from Vision to Change in Undergraduate Biology Education” at #AAASmtg: bit.ly/xnY182
    Sun, Feb 19 2012 11:57:06
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    At the undergraduate biology education session at #AAASMtg watching youtube.com/watch?v=PHmwZ9…
    Sun, Feb 19 2012 11:58:15
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    Did You Know? 3.0 (Official Video) -2009 Edition
    Wed, Apr 08 2009 09:55:40
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    Sorry I am missing talk by @researchremix at #AAASMtg – there were no seats in the back and so I went to biology education session
    Sun, Feb 19 2012 12:12:42
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    Suggestion to have “learning paragraphs” in biology education having students answer ? about what they learned that week #AAASMtg
    Sun, Feb 19 2012 12:14:21
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    As #AAASmtg session discussing the “Testing Effect” en.wikipedia.org/wiki/Test…
    Sun, Feb 19 2012 12:36:40
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    RT @phylogenomics: At #AAASmtg education session people using strange carbon based communication system http://pic.twitter.com/2Kk1Opgk
    Sun, Feb 19 2012 12:44:39
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    Watching this brilliant video is #AAASMtg science education session “Five Minute University” youtube.com/watch?v=kO8x8e… #brilliant #FatherGuido
    Sun, Feb 19 2012 12:44:49
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    Father Guido Sarducci’s Five Minute University
    Tue, Jan 23 2007 20:07:36
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    NoWatching “A Private Universe” at #AAASMtg Science Education session shar.es/gbyII
    Sun, Feb 19 2012 12:47:03
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    At #AAASMtg science education session discussing “Backward Design” flec.ednet.ns.ca/staff/Wha… emphasizes learning not teaching
    Sun, Feb 19 2012 12:53:48
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    Backward course design: 1) where should students be at end of course? 2) how KNOW they got there? 3) how help them get there? #AAASMtg
    Sun, Feb 19 2012 12:55:51
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    Quoted at #AAASMtg “If they sit and listen what they learn to do is sit and listen” Randall Phillis U Mass Amherst
    Sun, Feb 19 2012 13:00:57
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    Fish eye view of #AAASmtg science education session http://pic.twitter.com/RKg5ljUU
    Sun, Feb 19 2012 13:13:12
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    Panoramic view of harbor at #aaasmtg yesterday http://pic.twitter.com/g1HrhMXt
    Sun, Feb 19 2012 13:38:17
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    @lizabio @phylogenomics @thegreenelk Yeah, me too. That’s one way that Instagram can’t compete atm!
    Sun, Feb 19 2012 13:49:43
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    @phylogenomics @LouWoodley @thegreenelk Love that lens–it came out really well!
    Sun, Feb 19 2012 13:48:10
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    Hmm … does this newspaper know something about phylogenetics I need to know? #AAASMtg http://pic.twitter.com/K4JnS1VU
    Sun, Feb 19 2012 13:49:18
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    Wondering if #AAASmtg is planning to try and copyright me #aaasmtg http://pic.twitter.com/8Mi7Eaoo
    Sun, Feb 19 2012 14:04:42
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    Fish eye view of Entrance to convention center at #AAASmtg http://pic.twitter.com/UVeq3nwO
    Sun, Feb 19 2012 14:07:40
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    Bye bye #AAASmtg – hello lines at YVR http://pic.twitter.com/8RvlHMZE
    Sun, Feb 19 2012 15:02:26
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    Hmm – something wrong with restroom on my camera #whalefail #aaasmtg http://pic.twitter.com/dXJICxCO
    Sun, Feb 19 2012 15:08:29
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    Great meeting @PamBrierley, @phylogenomics and a bunch of other twits at the tweetup last night! #aaasmtg
    Sun, Feb 19 2012 15:47:01
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    Audio: Science Podcast, 17 February 2012 – #AAASMtg Special – Earth Microbiome Project @SpokenWord.org shar.es/goWFL
    Sun, Feb 19 2012 17:30:04
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    Strangest sighting for me at #AAASmtg – sign above urinal saying “The water is not intended for consumption” http://pic.twitter.com/oOzv9n2t
    Sun, Feb 19 2012 17:37:11
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    @phylogenomics I tweeted that yesterday – glad to know I am not the only person with their phone out while peeing!
    Sun, Feb 19 2012 18:38:57
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    I noticed that too! MT @phylogenomics: At #AAASmtg – sign above urinal, “The water is not intended for consumption” twitter.com/phylogenomics/…
    Sun, Feb 19 2012 17:54:50
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    Well @carlzimmer may not have been at #AAASMtg but his virus book was #GuardiansOfMicrobialDiversity http://pic.twitter.com/hjcIwWlG
    Sun, Feb 19 2012 17:38:42
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    Best attempt to connect to the local area at #AAASMtg – The Science of NHL Hockey http://pic.twitter.com/dgnNsngN
    Sun, Feb 19 2012 17:39:57
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    Cool model organism art at #NAIST display at #AAASmtg http://pic.twitter.com/6LVkjV0G
    Sun, Feb 19 2012 17:45:04
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    @phylogenomics oooh pretty, where is the #NAIST display?
    Sun, Feb 19 2012 18:52:12
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    @JennyCarpy may not be there anymore – was in the downstairs area with all the booths/posters
    Sun, Feb 19 2012 18:56:47
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    Second strangest sighting at #aaasmtg – biology conspiracy theorist handing out his theories http://pic.twitter.com/019s3AXZ
    Sun, Feb 19 2012 18:02:39
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    Scientists apparently do not like cauliflower #aaasmtg http://pic.twitter.com/ynH1l6LG
    Sun, Feb 19 2012 18:08:39
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    @phylogenomics Cauliflowerians ! Makes more sense than veganism or that caveman diet thing some people are doing…
    Sun, Feb 19 2012 18:12:27
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    @makischa me too
    Sun, Feb 19 2012 18:14:10
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    I understand completely… RT @phylogenomics: Scientists apparently do not like cauliflower #aaasmtg
    Sun, Feb 19 2012 18:13:39
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    Me and @lizabio at #aaasmtg holding up the world http://pic.twitter.com/WhOB7lkd
    Sun, Feb 19 2012 18:13:47
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    @phylogenomics @lizabio With telekinesis, no less.
    Sun, Feb 19 2012 18:44:21
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    Before trying to solve its problems ;) RT @phylogenomics Me and @lizabio at #aaasmtg holding up the world twitter.com/phylogenomics/…
    Sun, Feb 19 2012 18:49:39
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    Before trying to solve its problems ;) RT @phylogenomics Me and @lizabio at #aaasmtg holding up the world twitter.com/phylogenomics/…
    Sun, Feb 19 2012 18:49:39
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    @ejwillingham @phylogenomics We have special powers, Emily.
    Sun, Feb 19 2012 18:50:22
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    @lizabio @phylogenomics & we can access them w/o a paywall!
    Sun, Feb 19 2012 19:04:40
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    RT @phylogenomics: Completely brilliant: Crackpot Index bit.ly/luJ51 via @blakestacey #AAASmtg
    Sun, Feb 19 2012 18:13:33
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    We were there! RT @meganmansell: inspired by amateur birders, @phylogenomics held citizen microbiology workshop at UC Davis. #aaasmtg #emp
    Sun, Feb 19 2012 22:35:38
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    w/o a doubt the best aspect of #AAASmtg – giving my kids science schwag #GoScience post.ly/5TOjH
    Sun, Feb 19 2012 22:41:10
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    Posted slideshow w/ audio for my talk on “A Field Guide to the Microbes” from #AAASMtg youtu.be/yoD6Fs5yRdU #EarthMicrobiome
    Mon, Feb 20 2012 11:44:27
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    A field guide to the microbes – talk by Jonathan Eisen @phylogenomics at #AAASMtg
    Mon, Feb 20 2012 10:51:41
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    Report from @b0yle on.msnbc.com/wypvXo on #microbiome #AAASmtg. Join us 4/15-16 bit.ly/ISBsymp, featuring @JCVenter & @phylogenomics.
    Mon, Feb 20 2012 13:40:23
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    Strange “Seeing the elephants” conspiracy-esque document handed out at #AAASMtg post.ly/5UHgF
    Mon, Feb 20 2012 13:52:42
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    Strange “Seeing the elephants” conspiracy-esque document handed out at #AAASMtg
    Wed, Feb 22 2012 14:34:18
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    Most “@” mentions #AAASmtg ’12 con’t 4) @phylogenomics, 157 5) @erinbiba, 154 need4feed.com
    Mon, Feb 20 2012 16:30:27
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    The Tree of Life: Jack Gilbert @gilbertjacka clarifies comments at #AAASMtg re: opening windows, cleanliness… goo.gl/fb/0ux54
    Mon, Feb 20 2012 19:16:21
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    @gilbertjacka all I can say is ‘uh oh’
    Sun, Feb 19 2012 22:34:45
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    @phylogenomics :-) makes me laugh though – you think this will come back to bite me?
    Sun, Feb 19 2012 22:35:32
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    @gilbertjacka there is no doubt – really – that this will come back to bite you
    Sun, Feb 19 2012 22:36:03
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    @gilbertjacka so I hear
    Sun, Feb 19 2012 22:36:45
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    Jack Gilbert @gilbertjacka clarifies comments at #AAASMtg re: opening windows, cleanliness & microbes
    shar.es/gfBcH
    Mon, Feb 20 2012 19:23:10
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    Guess I should stop eating dirt and rubbing LB agar into cuts then.
    MT: @gilbertjacka clarifies comments at #AAASMtg shar.es/gfBcH
    Mon, Feb 20 2012 19:45:48
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    Ooo thanks! RT @phylogenomics: Slideshow w/ audio of my talk on “A Field Guide to the Microbes” from #AAASMtg goo.gl/fb/B6zRk
    Tue, Feb 21 2012 03:46:26
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    The Tree of Life: Slideshow w/ audio of my talk on “A Field Guide to the Microbes” from the AAAS Meeting #AAASMtg bit.ly/x0fMxF
    Tue, Feb 21 2012 04:59:47
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    For @phylogenomics, from #AAASmtg http://pic.twitter.com/uXfHCXen
    Tue, Feb 21 2012 14:49:27
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    And here’s the other one, @phylogenomics http://pic.twitter.com/ugdmPKce
    Tue, Feb 21 2012 14:54:38
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    More #AAASmtg stats: @CanadaAAAS, @phylogenomics and @ericmjohnson most RTed/mentioned.
    Wed, Feb 22 2012 11:20:08
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    w/o a doubt the best aspect of #AAASmtg – giving my kids science schwag #GoScience post.ly/5TOjH
    Sun, Feb 19 2012 22:41:10
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    w/o a doubt the best aspect of #AAASmtg – giving my kids science schwag #GoScience
    Wed, Feb 22 2012 14:34:18
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    Love the image from MBARI in this article: Scientists map the world’s microbes shar.es/gWOOV
    Mon, Feb 20 2012 11:09:24

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