Tag: meetings

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.  
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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

P209

P223 P221 P219 P217 P215 P213 P232 P231 P229 P211 P225

See the full gallery on Posterous

p227.mov Watch on Posterous

–

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Having fun at banking session at #compass11

p186.mov Watch on Posterous
P188

P190 P192 P196 P198 P200 P201

See the full gallery on Posterous
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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  
  • 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? 
  • 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
  •  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  
  • 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

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.



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” 
  • 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” 
  • Ochman: Why aren’t there lots of pseudogenes in most bacterial genomes? B/c there is a mutation bias towards deletions
  • Ochman referencing “Bacterial genome size reduction by experimental evolution”  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 
  • Ochman referencing “The consequences of genetic drift for bacterial genome complexity” 
  • 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  prof. Paul Baumann 
  • 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 
  • Moran discussing the Tremblaya genome which has recently shown up in Genbank 
    • : @phylogenomics Tremblaya is awesome. John McCutchoen is the man – hope this is published soon.
    • : @phylogenomics 58% GC in an insect symbiont – simply weird. McCutcheon talked about this at SGM Insect Symbiosis in Harrogate, UK in April.
    •  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 
  • 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 
  • 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 Pubmed
  • 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
    •  @phylogenomics Limit on “genome size”. He means gene number (which does correlate in bact/arch but not euk)
    •  Sorry .. He is only discussing bacteria and archaea … So here it does correlated w/ genome size
    •  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
    •  yes but this was a bit of a big deal … Press coverage … Nature paper, etc etc …
    •  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 … 
  • 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 microevolution
  • 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 elements
  • 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 Direct which is both  and has open review
  • Koonin has a new Book: The Logic of Chance: The Nature and Origin of Biological Evolution: ProQuest Tech Books

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:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Travel and meeting notes from #IndoorAir2011 in Austin Texas #microBEnet

Here are some quick notes from my trip to Austin Texas for the Indoor Air 2011 meeting.

About the meeting:
I got involved in helping organize a session at this conference as part of my microBEnet project.  More on the planning and the meeting later but here are some quick notes just to get them out there.  I wrote a bit about the run up to the meeting in the following posts:

The meeting.
Below are some notes about the trip with twitter posts, pictures, and a few comments.  I will post later with some more “scientific lessons learned” and such.  But wanted to get this out there before I forgot details.

Headed out June 6.
Was going to head out June 7 but decided to head out late on June 6 so I could get to the meeting a bit earlier.  I am posting my tweets below as a guide to the trip.  Tweets are highlighted in yellow.

Had a two plus hour layover in Las Vegas airport.  What a horrible place with all the noise, the slot machines, and such.  So I finally found a place that was reasonably quiet for dinner.  Plus it had the hockey game on so I was happy.

  • How to have fun at Vegas airport – sit near security & watch ; apparently what happens in Vegas stays at security
  • @PsiWavefunction sorry – you missed the hidden joke – I can’t tell story because what happens at security …. twitpic.com/582r4r

When I got on the plane to Austin, I got the window seat in the emergency exit row that has the most room.  And eventually someone came to sit in the middle seat.  And he seemed, well, a bit off.  I did not realize why until a Southwest attendant came to ask people if they could ha\ndle the duties of the exit row and the attendant started asking this person when he had his last drink.  And then they decided he was drunk and nicked him out of the exit row. 
  • Wow, on plane about to leave for Austin; southwest attendant moved person out of exit row next to me b/c he was drunk twitpic.com/582uko
  • Good call Southwest – keeping planes safe (see last post)
Arrived in Austin.  Had to wait a bit for a shuttle to the “Airport Hilton” which was weird to me because they told me it was in the terminal.  Liars.  So I snooped around at the pet bathroom area:

Finally got to the hotel – was very very tired.  And I took some pics and went to sleep.

Day 2: 
Got up pretty late and had some coffee in the cafe in the lobby and took some pictures

Then I headed out to downtown to my new hotel.  Nice view from my room.

And I met Jason Stajich at the hotel and then David Hillis from UT Austin picked us up to go to lunch (well, David came to pick me up but I had met up with Jason and invited him, assuming it would be OK with Hillis).  Hillis is truly one of my favorite people in all of science.  He took us to a good Mexican place nearby.  And we talked about all sorts of things over lunch.  Hillis wrote a funny post about this on Facebook but since it is not “public” I cannot link to it here.  Mostly he was commenting on the strange looks we got when talking about microbes living in and on people. 
And then Hillis dropped us off and Jason came by my room while I grabbed some stuff to take over to the convention center. 

We then walked on over to the Convention Center and as always I took some pics of the interesting stuff along the way:

I registered and dropped in on some talks:
  • Learning about affect of copper vs Aluminum surfaces in HVACs on microbial growth: copper seems to control growth better #IndoorAir2011
Did not post much since I did not yet know the rules about twitter usage at the meeting.  I ran back to my hotel to get something I forgot and then headed back to the Convention Center again.  This is one reason I like staying in hotels right next to meetings.

On my way out I bumped into Norm Pace who was on his way in.
After a few minutes at my hotel I returned to the Convention Center for more talks and meeting people:
I went to a talk or two but did not last long.  Not enough on microbes this day. And so I headed to the product show with Russell Neches a PhD student in my lab.  

Finally there was a session that appealed to me:
  • Yuguo Li, Bill Nazaroff, Hal Levin, Charlie Weschler &; Jan Sundell now discussing continuity between indoor & outdoor air #IndoorAir2011
  • Charlie Weschler “Outdoor measurements are useless in exposure analysis? No! Ozone” When outdoor ozone up so is indoor #IndoorAir2011
  • Weschler: Why care about ozone? Morbidity and mortality go up when ozone does #IndoorAir2011
  • Bill Nazaroff discussing indoor vs outdoor exposures and a tutorial on particles which come in a whole zoo of forms #IndoorAir2011
  • Nazaroff working on models to predict indoor exposure from measures of outdoor air #IndoorAir2011
  • Having serious jargon/context #fail issues at talks at #IndoorAir2011 tho Nazaroff from Berkeley nearly flawless in being jargon free #wow
  • RT @IAQnerd: “43 chemicals found in virtually every pregnant woman” #indoorair2011 #TSCA #NAGP #holisticmoms #healthychild
  • My collaborator on microbe.net #microBEnet Hal Levin now discussing microbes indoor/outdoor #IndoorAir2011
  • It is funny that at the #IndoorAir2011 sessions there have been troubles with WindowsOS – do indoor air researchers dislike windows?
  • Funny notion from speaker at #IndoorAir2011 – windows define buildings as much as doors so why not say we are “Inwindows”
  • Speaker at #IndoorAir2011 “Indoor air is much more important than outdoor air” but $$ is in outdoor air – though I & others don’t agree
  • @phylogenomics VIA @ryneches Richard Corsi has given us permission to tweet, advises against emulating congressmen. #indoorair2011
  • @B_EMC Yuguon Li
  • @B_EMC actually I think it was Jan Sundell who said that

And then eventually I headed to dinner with Jason Stajich and took some more pics.  We wandered around town a bit before ending up at the Shoreline Grill and David Coil,  a post doc from my lab, showed up a bit later to meet us there.

Day 3

Got up reasonably early and took some pics from my room in the AM

Then headed over to the conference center as soon as I could because Craig Venter was on the agenda for the AM session.

Session on Microbiomes of the Built Environment.  First speaker – Beverly Wright.
Next speaker – J. Craig Venter.
  • Next up at #IndoorAir2011, Craig Venter – as an aside his most recent pub is one w/ me on stalking the 4th domain http://tinyurl.com/64rtyvc
  • Jesse Ausubel – says there must be meaning in the universe b/c speaker at Indoor Air meeting is named “Venter” #IndoorAir2011
  • Ausubel says he is “an advertisement” for Craig Venter and gives a bit of an biography of Craig in 2 minutes #IndoorAir2011
  • Ausubel gave a very glowing, flowing, comprehensive, yet remarkably short intro to Craig Venter #IndoorAir2011
  • Venter: discussing converting the analog code of DNA into a digital code of data “digitizing DNA” #IndoorAir2011
  • Venter used three slides to cover the history of genome sequencing #IndoorAir2011
  • Venter predicts in the future companies will pay people to sequence their genomes to get the data #IndoorAir2011
  • Venter discussing microbes in mouth says “think about that while the person next to you is coughing, or you are kissing them” #IndoorAir2011
  • Venter suggesting that esophageal cancer samples have unique microbial composition – says cause vs effect not known #IndoorAir2011
  • Venter: w/ metabolomics can track which chemicals in blood come from human metabolism vs. food vs. bacteria/microbes #IndoorAir2011
  • Venter: you are not just who you are and what you eat but also what you feed your bacteria #IndoorAir2011
  • Venter: some think his most brilliant discovery was figuring out how to sail around sea and do science at same time #IndoorAir2011
  • Venter: emphasizes the #PLoSBiology collection on ocean metagenomics including his/my GOS papers ploscollections.org/article/browse… #IndoorAir2011
  • Venter showing reference genome plots of Doug Rusch such as ploscollections.org/article/slides… #IndoorAir2011
  • Venter showing Jeff Hoffman sampling frozen lakes in Antarctica – massive amounts of biomass and biodiversity #IndoorAir2011
  • Venter saying very low diversity in microbes 1mile deep in ocean/crust — suggests that UV light may be driver of diversity #IndoorAir2011
  • Venter: working on air microbes – it was much harder than anticipated and thanks Sloan foundation for their patience #IndoorAir2011
  • Venter: very little biomass recovered from indoor air; have to run samplers for long time; but they get contaminated; #IndoorAir2011
  • Venter: v. hard to get water clean enough (i.e., without DNA contamination) to use in studying samples w/ very little biomass #IndoorAir2011
  • Note – I don’t buy the “UV light” connected to diversity explanation Venter just gave at #IndoorAir2011 – just reporting what he is saying
  • @subsurface_life he was not talking about richness but variation among close relatives; says there is less genetic diversity w/in species
  • Venter: now looking at samples from the Space Station #IndoorAir2011
  • Venter: in New York Indoor Air – the major source of DNA is human; #2 is rodent; microbes are a small % #IndoorAir2011
  • Venter: outdoor air in NYC most DNA is rodent, human a bit less than in indoor air #IndoorAir2011
  • @subsurface_life millions of reasons other than UV – just posted a separate tweet saying I don’t believe it
  • Venter: in NYC there is lots of iron in the outdoor air; “if you are anemic that might be good but otherwise probably not” #IndoorAir2011
  • @pzmyers apparently, though unclear how they sampled — did say that at Scripps Pier the #1 signal was insect
  • @Toxicpath @pzmyers unclear how the air sampling worked so not sure why they were getting so much rodent/human DNA vs. insect, bacterial
  • Venter has now shifted to discussion synthetic biology #IndoorAir2011
  • Venter shows a very very simple animation and says “We have this very sophisticated movie to show this” #ScienceHumor #IndoorAir2011
  • Venter: creating prokaryotic chromosomes in yeast; waiting for Norm Pace to learn him about “just say no to prokaryote term” #IndoorAir2011
  • Venter: says massive growth in population means that new biotech. dvlpmts (e.g., synthetic biology, fuels, etc) are needed #IndoorAir2011
  • Venter ends with discussion of ethics and synthetic biology #IndoorAir2011
  • They just asked Venter @ryneches twitter question “Can I have your boat?”#indoorair2011
Then Bill Nazaroff
  • Now starting session on “Microbiomes of the Built Environment” supported by @SloanFoundation -1st speaker is Bill Nazaroff #IndoorAir2011
  • Nazaroff “Newton meets Darwin and the Indoor Microbiome” discussing sociology of science #IndoorAir2011
  • Nazaroff quoting John Harte from “Towards a synthesis of the Newtonian and Darwinian worldviews” #IndoorAir2011
  • Here is a link to John Harte’s excellent paper on Newtonian vs Darwinian synthesis http://bit.ly/lBrK4C #IndoorAir2011
  • Note I worked at RMBL for two summers when John Harte was there – I really like him – and lived w/ his son there #IndoorAir2011
  • Nazaroff: successful collaborations come from small groups working on close contact rather than large teams #IndoorAir2011
  • Nazaroff: finding ways to keep egos under control is a key issue in scientific collaborations #IndoorAir2011
  • Nazaroff: DNA based methods are game changing in Indoor Microbiome studies but we still need to ask the right questions #IndoorAir2011
  • Nazaroff discussing work w/ Jordan Peccia looking at microbial surveys in classrooms as well as BIMERC project at Berkeley #IndoorAir2011
Then Norm Pace
  • Now up, the one and only Norm Pace – discussing rRNA surveys of human occupied indoor environments #IndoorAir2011 #Oneofmyscienceheroes
  • Pace: his job here is to help people transition from whatever microbiology they learned in a past life to modern microbiology #IndoorAir2011
  • psgcom #indoorair2011 check out www.microbe.net for more on Sloan Foundation funded work on Microbes of the Indoor Environment #microbenet
  • Pace: lots of microbes in tap water (good source of protein) but to understand those microbes you need to use sequences #IndoorAir2011
  • Here is a list we made of Sloan Foundation projects on microbes in the built environment microbe.net/grantees/ #microBEnet #IndoorAir2011
  • Pace: using fluid impingers to sample air – need ones with massive throughput #IndoorAir2011
  • Pace: key point – for studying microbes via DNA cleanliness (i.e., no contaminating DNA) is more important than sterility #IndoorAir2011
  • Pace: Indoor air microbiology is mostly about microbes shed by humans #IndoorAir2011
  • Pace: key for future of IndoorMicro is bring together people from different fields; that’s why we created http://microbe.net #IndoorAir2011
M. Taubel.
  • Next: M. Taubel on diversity and dynamics of bacteria in house dust #IndoorAir2011
  • Taubel: Interested in “hygeine hypothesis” and how exposure to microbes affects asthma, allergy, automimmune dvlpmt #IndoorAir2011 #fb
  • @Chris_Evelo Well, don’t forget each human cell has a lot more DNA than each microbial cell (well, for most microbes) #IndoorAir2011
  • Taubel referencing bacteria-dust studies in BMC Microbiology 8:56 and J. Allergy Clin Immunol 124: 834 #IndoorAir2011
  • Taubel: not going into details of methods b/c 90% of people understand methods and 10% only care about results #IndoorAir2011
  • Taubel used a term I have not seen: SLOTUs – species level operational taxonomic units; though I note I 1st read it as SLUTS #IndoorAir2011
  • Taubel: mattress dust has lower richness of bacteria (# of species) than floor dust #IndoorAir2011
  • Taubel: most of what they find in house dust is similar to microbes found on people #IndoorAir2011
Denina Hospodsky

Lew Harriman

  • Next speaker is Lew Harriman from a consulting company http://MasonGrant.Com: focused on water availability #indoorAir2011
  • Harriman: buildings are designed to be dry, not damp; though I note damp doesn’t always mean bad #IndoorAir2011
  • Harriman: measurements of relative humidity usually focus on air but probably should measure on surfaces #IndoorAir2011
  • Now up Miia Pitkaranta from Finland: seasonal variation in microbes in buildings & affect of H20 biocenter.helsinki.fi/bi/dnagen/indo… #IndoorAir2011
  • Miia Pitkaranta refs on Indoor Microbiology AEM 74:233 & BMC 8: 56 #IndoorAir2011
  • Pitkäranta: species richness in dust is very high; ~ 10-20% of species cultivable; phylogenetic diversity of fungi high #IndoorAir2011
  • Pitkäranta: spatial variation in microbes in dust from different parts of buildings very high #IndoorAir2011
Gunilla Bok
  • Next at #IndoorAir2011 Gunilla Bok: Identification of mould fungi by blast similarity searches and phylogenetic analysis
  • Kudos to meeting organizers of #IndoorAir2011 for diversity of speakers: young -> old; diverse country, genders, etc
  • Next & last this AM: Alina Handorean on phylogenetic analysis of microbes from bioaerosols from a flooded building #IndoorAir2011
Hal Levin
  • Hal Levin, my collaborator on #microBEnet http://microbe.net is now talking at #IndoorAir2011
  • Hal Levin trying to determine what is known about environmental factors that influence indoor microbial ecology #microBEnet #IndoorAir2011
  • Levin: some environmental factors affecting microbial ecology: humidity, temp, ventilation, surfaces, chem composition, pH #IndoorAir2011
  • Nazaroff points out that human occupants have profound influence on microbial ecology #IndoorAir2011
  • Another speaker suggested building age is important in microbial ecology indoors #IndoorAir2011
Mike Frankel
  • Now up Mika Frankel discussing influence of season and sampling methods on inferred microbial composition #IndoorAir2011
  • Frankel sampling in airborne and settled dust in four rooms in five homes #IndoorAir2011
  • Personal opinion – I am not a big fan of very short talks at meetings – I like 20-30 minutes not 10-15 #IndoorAir2011
Brendan Bohannan
  • Now up Brendan Bohannan – arguably one of the greatest speakers in the whole field of microbial ecology #IndoorAir2011
  • Bohannan is involved in the BioBE center (Biology and the Built Environment Center) at U. Oregon biology.uoregon.edu/biobe/?p=124 #IndoorAir2011
  • Bohannan discussing “How Communities Assemble”: two major categories – sampling & filtering #IndoorAir2011
  • Bohannan: filtering in microbial ecology is fact that some environments support growth of some taxa over others #IndoorAir2011
  • Bohannan: sampling in microbial ecology is the idea that in some cases microbes you see are just sampling from larger pool #IndoorAir2011
  • Bohannan: microbes in buildings are mostly from sampling/filtering from two pools – outdoor air & human occupants #IndoorAir2011
  • Bohannan: trying to understand how microbial communities assemble in a hospital #IndoorAir2011
  • Bohannan: indoor air is different from outdoor air (he knows this is not surprising); outdoor much more diverse #IndoorAir2011
  • Bohannan: are indoor samples subsets of the species found outdoors? No – appear to be very distinct types of microbes #IndoorAir2011
  • Bohannan: comparing indoor & outdoor air microbes to those in soil, humans, etc; indoor air more like skin; outdoor like soil #IndoorAir2011
  • Bohannan: microbes in some rooms like outdoor air/soil, in other rooms like people; #IndoorAir2011 differences may be due to ventilization
  • Bohannan: higher the airflow in room, the lower the frequency of organisms closely related to human pathogens #IndoorAir2011
  • Bohannan: suggests architects in future could design buildings with “microbial comfort” in mind and not just human comfort #IndoorAir2011
Jordan Peccia
  • Norm Pace points out that should be very careful w/ term pathogen esp. when we don’t know actual pathogenicity #IndoorAir2011
  • Jordan Peccia discussing growth of Aspergillis spores #IndoorAir2011
  • Note -before Pace said should say “organisms related to pathogens” I said “organisms closely related to human pathogens”#IndoorAir2011 #Ego
  • Peccia – are all Aspergillis spores the same (in terms of allergenicity and other things)? #IndoorAir2011
  • After talks the whole of #IndoorAir2011 is heading to the Salt Lick Bar-B-Que Restaurant saltlickbbq.com #NotVegetarianFriendly
  • Peccia: culturability & qPCR can significantly (5-50x) underestimate allergenicity of A. fumigatus spores produced at low T° #IndoorAir2011
  • If I had videos of Brendan Bohannan’s talks I have recently seen, I would make a mashup & use it for my talk tomorrow at #IndoorAir2011
Ming-Ching Liang

Then I headed back to my hotel for a bit and took a few more pics.

I decided not to go to the Salt Lick BBQ party mostly because I wanted to stay near the water.  And so eventually a few of us gathered together and I found a place near the hotel/convention center.  Jason Stajich and I got there early and went to Clive Bar which was very nice. 

And then Shannon Williamson showed up and we eventually made it across the street to a little “cart” restaurant that was rated very highly called Cazamance.

  • Of course I wants to eat here with a “Tree of Life” logo – Cazemance – food was great (@ Cazamance) [pic]: http://4sq.com/kUJDm6

I had a bit of insomnia as usual when travelling and was then woken up when I finally fell asleep by a helicopter nearby:

Day 4

Got up early again.  Headed out to breakfast and coffee and worked on my talk for a while.  There was a session this AM in which I was speaking.  The session was on microbiomes of the built environment and it was coorganized by Hal Levin as part of my microBEnet project.

Posted my slides (which I had worked on over breakfast)

Jesse Ausubel gave the opening talk:
  • Jesse Ausubel from Sloan Foundation up at #IndoorAir2011: the Known, Unknown & Unknowable (KUU) Framework to developing a research agenda
  • Ausubel: Sloan Foundation started by ex-GM head- though no connection now, he notes maybe we should study microbes in cars #IndoorAir2011
  • Ausubel: built environment of course critical to development – the more we understand it the better #IndoorAir2011
  • Ausubel refs Josh Lederberg & his interest in biodefense – if we want to detect anthrax in air need to know the background #IndoorAir2011
  • Sloan originally interested in general survey of microbes in the built environment & basic science in this area #IndoorAir2011
  • Key to Sloan $$$: they are seed money/science venture capital – they hope it leads to “powerful organized gang” i.e. a field #IndoorAir2011
  • Ausubel: what can Sloan do? funds specific projects as well as the “glue” to hold projects together e.g., http:microbe.net #IndoorAir2011
  • Ausubel: Sloan Foundation very supportive of open science including #openaccess to literature and sharing in various ways
  • Sloan has supported many #PLoS activities including the new PLoS Hubs in Biodiversity http://hubs.plos.org/
  • Ausubel says we should think about “macroprojects” that need collaboration- asks if there are BigScience needs #IndoorAir2011
  • Ausubel says it is the unknown that sets the research agenda for fields & allows for marketing to get more resources #IndoorAir2011

Aino Nevalainen

  • Aino Nevalainen : introducing microbiology and the indoor environment #IndoorAir2011
  • “I have feeling I have to do a 100 meter sprint on a distance that is a marathon” – i.e., too much to cover, too little time #IndoorAir2011
  • Nevalainen: quoting Leviticus regarding leprous plague and what to do Leviticus 14: 33-38, 39-42, 43-47 #IndoorAir2011
  • Nevalainen: priests were the first indoor air consultants, regarding quarantine and leprosy #IndoorAir2011
  • Nevalainen refs. MH Gordon 1904 Bacterial test for estimating pollution of air. Sppl. for 32. Ann Rep of the Local Gvmt Board #IndoorAir2011
  • Nevalainen refs Richards 1954 J. Allergy 25: 429 – Atmopspheric molds spores in and out of doors #IndoorAir2011
  • Nevalainen refs JACI 62: 22-26 Hirsch et al. 1978, Ann Occup Hyg 27: 341-358 Ager and Tickner 1983, Lidwell and WC Noble 1975 #IndoorAir2011
  • Nevalainen refs studies of humans as source of microbes in air: Sciple etal. ’67, Duguid & Wallace ’48, Noble & Davies ’65 #IndoorAir2011
  • Nevalainen refs nice reivew of microbial ecology of skin by Roth and James 1988: IDs factors modifying normal flora #IndoorAir2011
  • Nevalainen sources of indoor microbes: outdoor air, uses of buildings (people, pets, etc), microbial indoor habitats #IndoorAir2011
  • Nevalainen does not mention plants as a source of indoor microbes – something I am interested in studying … #IndoorAir2011
  • Nevalainen: aerosols in indoor air behave in same general way as those outdoors #IndoorAir2011
  • Nevalainen: microbial exposure associated w/ health, both positive (e.g., protection agst allergy) negative (e.g., pathogens) #IndoorAir2011
  • Nevalainen: microbes growing on building surfaces are “bad microbes” in the sense that they should be an area of concern #IndoorAir2011
  • Nevalainen: the way ahead – more info on exposure & health; more info on whether culturable are good models for all microbes #IndoorAir2011

Then I gave my talk and we had multiple break out sessions which seemed to go well discussing the future of indoor microbiology studies.

Then headed to a dinner I hosted for Sloan Funded researchers working on microbiology of the built environment.  Again to the Shoreline Grill (I did not realize this is where we were going to have the big dinner when I had gone there a few days before)

Then drinks and people started to show up

Then dinner with a mini break in the middle to see the bats which fly out from under this bridge nearby.

Then back to dinner and dessert:

  • Best question of the day “So what about the viruses” #microBEnet – don’t ignore the viruses

More dinner pics

Then to drinks at the Four Seasons and eventually to sleep:

  • Cool – the Four Seasons in Austin has a cowboy boot vending machine twitpic.com/59euel

At the airport I bumped into William Gunn from Mendeley:

I made a few last posts:

And headed home

To where I was greeted by my family and my cats:

Then I posted some final links:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Some quick notes on #Synbio5: Synthetic Biology 5.0 at Stanford

Well, just got back from Synthetic Biology 5.0 at Stanford.  I don’t really have time to do a thorough job with a blog post but I will try to fill in some details here.

1. Got invited by Natalie Kuldell in April to participate in an education workshop for the meeting.  Eventually said yes, but only after deciding to not go to the Earth Microbiome Meeting in Beijing. I said yes in part b/c it was close by home but also b/c of the people Natalie invited to be on the panel.  She wrote in the invitation email:

Other panelists who have confirmed their participation in this session are from Understanding Science/Understanding Evolution (Juday Scotchmoor), Nature Education (Ilona Miko), Science for Citizens (Darlene Cavalier), GenSpace (Ellen Jorgenson), and Hong Kong University of Science and Technology (King Chow).

And well, of the ones I knew on the list, they all were great.

2. Had a conference call (very brief) in June to discuss the session.

3. Headed out to Stanford very late Tuesday night – and thus missed the Slam session that night.  I got to my hotel at about 1:30 AM.

4. I woke up early enough to hop on my bike and ride on over to the meeting.  I was a PhD student at Stanford and had brought my bike in the hopes of going for some rides around town.  I took some pics on the way in:

Got to the meeting and of course posted a few tweets

5. Then went in to the session.  I went up to the front and said hello to Eric Lander and talked to him about my recent PhD student Amber Hartman who has taken a job in the White House Office of Science and Technology Policy.  I then said hello to some of the others in the session and took a seat in the front row and started tweeting and taking pictures.




  • phylogenomics: Endy refs quote of Eric Lander’s from after human genome proj: “Genome – bought the book – hard to read” twitpic.com/5bxgb7 #synbio5
  • phylogenomics: John Glass: he is very proud of being involved in making 1st synthetic genome – if he were a goat he would infect himself w/ it #synbio5
  • phylogenomics: Lander asks “What are the ret challenges of synthetic biology” – need a list like Hilbert’s math challenges to shape field” #synbio5
  • phylogenomics: John Glass discussing history of synthetic genomics #synbio5and why they started working on mycoplasmas http://t.co/aVuNino



http://video.google.com/googleplayer.swf?videoUrl=http://v8.nonxt3.googlevideo.com/videoplayback?id%3D7fc1934b8f02267f%26itag%3D5%26ip%3D0.0.0.0%26ipbits%3D0%26expire%3D1308459304%26sparams%3Did,itag,ip,ipbits,expire%26signature%3DAED7ADADB5710F852D6CC278C256EF0913787150.24C77B960F67D0077AFCE6BDD5C2BB709A72ABC0%26key%3Dlh1

  • phylogenomics: RT @peccoud: RT @synthaes: how do we keep synthetic genomics open source? vital – jef boeke #synbio5 So many aspects: data, software, sequences
  • phylogenomics: Love how speaker at #synbio5 trying to push for power of synbiology and Eric Lander keeps saying “The genetics told us that” #gogenetics
  • phylogenomics: Eric Lander is one of the best panel moderators I have ever seen – except maybe Robert Krulwich – #synbio5 – great job pushing discussion
  • drkahaynes: ITA He’s great RT @phylogenomics: Eric Lander is one of the best panel moderators I have ever seen #synbio5
  • phylogenomics: Pam Silver says that the virome is fascinating and needs more looking into #synbio5
  • phylogenomics: Lander has just gone through effective population size Vs. Selective coefficients #math-at-9am #synbio5
  • phylogenomics: RT @peccoud: #synbio5 John Glass, we have no idea how to design a genome? Would studying evolution help? Not sure.
  • phylogenomics: The synthetic biology express – Drew Endy hand delivering questions to panel #synbio5 http://t.co/soIpd3c
  • phylogenomics: Lander fo abstracts for future science – some awesome ones – Pam Silver says “photosynthetic humans developed for travel to mars” #synbio5
  • phylogenomics: Alica Jackson from DARPA announcing DARPA is getting into synthetic biology in a big big big way w/ “Living Foundries Program” #synbio5
Then there was a break and I got to talk to a few key people including Alicia Jackson from DARPA who I have been playing a bit of phone tag with.  I also got to meet some people I only knew online/via twitter like Erika Hayden.  





And then back in to the next session and more tweeting:




  • phylogenomics: Church wants to do fluorescent in situ RNA sequencing #synbio5– note he says this was original goal of his development of next gen methods
  • phylogenomics: Now up Alice Ting from MIT discussing technologies for detecting and analyzing proteins in living cells #synbio5
  • phylogenomics: Ting: there is a need for new protein labeling methods especially ones that add chemicals to specific amino acids of proteins #synbio5
  • phylogenomics: Ting: developed probe incorporation mediated by enzymes method #synbio5
Then I did indeed go for a bike ride (at lunch time)



I rode up alpine road – not too far – maybe 8-9 miles up and then 8-9 miles back.  But it was nice to get out and back on the roads of my semi-youth. 

And then back to the meeting (after changing shirts …) where I caught Pam Silver talking (note – Silver is one of my favorite people in biology – brilliant – really funny – down to Earth – etc; second note – she grew up in the area near the meeting and told some good stories outside in the breaks about skateboarding around Stanford Campus).

I then stopped tweeting because my phone battery died and I had to get back to my hotel to take a shower.  So I took a little break.  And then returned for the poster session where I really only ended up seeing one poster, because it was so awesome:


I spoke to Karmella for a while and then to some others.  And eventually I headed back to the hotel to crash because I was pretty beat.  I had dinner and then went back to my room and blogged about Karmella:
And went to sleep.

Then, at 4 AM the hotel alarm went off waking me up.  It eventually went off again while I was still trying to get my act together to get out of the room. And then it went off again a few minutes later.  I did not really get back to sleep.  So of course I posted something
  • phylogenomics: Thanks Westin in Palo Alto, the two false fire alarms at ~4 AM made my day; though one good thing:they did prove their alarms work #synbio5
I eventually went downstairs and decided to check out of the hotel and skip the Friday part of the meeting because I was just dragging.  So I checked out and complained about the alarm and got a free breakfast.  So I left my bike and suitcase at the front desk and went to breakfast where I saw Eric Lander also eating.  I did not want to bother him too much but I stopped by and said hello and then asked if he has seen the painted poster and he had not.  So I showed him pics and he asked if I could email him more detail because he wanted to invite Karmella to display her work at the Broad.  Eventually I drove on to campus to go to the AM talks.

I got there in the middle of a talk



So I went to the posters again and took some more pics of Karmellas poster so you could see the canvas.



I also got a picture of someone taking pictures of all the posters – which seemed a little lame.  I note I asked for permission from Karmella before taking pictures of her poster.



I then went to a talk or two and spent a bunch of time sitting outside talking to various people.  I pretty much always like meeting and talking to people over going to talks in overheated conference rooms (note to Stanford – if you want to host meetings in June get some f*$&% air conditioning in your rooms).  Also note – it may not be the best idea in the world to put out lunch boxes in the sun at 10:30 AM.


Eventually a group of us headed over to the side room where the Education session was going to be held:

The education session seemed to go quite well.  I will try to post more on it later but I note it was videotaped and the video will supposedly be posted.  It was great talking to the people on the panel and meeting some of the interested parties in the crowd.

And then after a group of us sat down for some sodas/tea and chatted.  It was good to get a few minutes with people dedicated to outreach and education.  And then to posters where I saw Marc Facciotti from Davis as well as a few other people I knew.  And finally to home:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Opening up one’s eyes to other fields (cross-posting from #microBEnet)

Cross-posting this: Opening up one’s eyes to other fields which I posted originally on the microBEnet blog.

I spend most of my time working on biology.  I like to think I cover lots of breadth within biology and I probably do – microbes, evolution, ecology, human health, pathogens, symbioses, forensics, genomics, bioinformatics, and more.  But nothing like really looking at other fields to realize how narrowly focused one is.

And that is what has happened to me since I took on the “microBEnet” project trying to foster communications and collaborations on microbiology of the built environment. I now pay much more attention to anything that might have a connection to “Building Science” in one way or another.  Not only did I just go to an Indoor Air meeting, but I keep discovering more and more stuff right near home that I was not aware of before.  For example – I just got sent this news link from Aaron Darling in my lab: UC Davis News & Information :: History of sciences in architecture subject of Mellon Foundation winner’s study.  Previously, I would definitely not have been paying much attention to architecture and history of science.  But now seeing other people at UC Davis working on the Built Environment just makes me think about how I can build connections with them and talk to them about buildings (and other built environments) and possibly, one day, about the microbes that are in them.

Which brings me to another story.  At the Indoor Air meeting earlier in the week in Austin, Texas, when heading to the conference center I got into a conversation with someone looking for the registration desk.  After showing her where to go she asked where I was from and I said “UC Davis.”  And it turns out – she was too.  Turns out, this was Deborah Bennett, who I had heard mentioned the evening before but had not heard the whole name.  I just knew someone else at the meeting was from Davis.   Deborah is at the UC Davis School of Public Health and works on some really interesting stuff.  And since UC Davis is so big (some 2500 or so faculty I think) – it is not always easy or simple to find people even if you might have a connection to them.

So anyway, just a little commentary on how I find it fascinating to see for the first what was in a way right before my eyes.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–