Tag: Misc.

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.

——–

Fun with a scanner – 1998 press release from Wellcome Trust re: Celera

Just found this in an old folder on a different topic.  It is a press release from the Wellcome Trust that was handed out at the Cold Spring Harbor Genomes Meeting in 1998 in response to the announcement from Venter et al. that they were starting a company to sequence the human genome.

——–
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.

——–

Ahh … Pubmed Central. I love you. In many ways. But alas, not today. #openaccess

Been having some challenges with Pubmed Central recently.  What is Pubmed Central?  If you don’t know, and you have anything to do with the life sciences in any way, you should learn.  A good place to learn is on their info page here.   Here is the summary:

PubMed Central (PMC) is a free archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health’s National Library of Medicine (NIH/NLM). In keeping with NLM’s legislative mandate to collect and preserve the biomedical literature, PMC serves as a digital counterpart to NLM’s extensive print journal collection. Launched in February 2000, PMC was developed and is managed by NLM’s National Center for Biotechnology Information (NCBI).

It is a fantastic resource.  Alas, there is one major limitation.  Mostly it is an archive of papers submitted by publishers.  Some publishers do not submit their material there.  Fortunately, there is now a way around this.  Author’s can submit their own papers to PMC.  However, there is some caveats to this — there are severe restrictions on what one can submit.  In the past I was aware of one of these caveats – the work in the manuscript has to have been at least partially supported by NIH funds (well, there is a way to submit if supported by the Wellcome Trust to).  To submit NIH supported work, you have to use the NIH manuscript submission system.  Why they won’t take papers supported by other funding agencies I do not know.  Imagine if Genbank only took sequences inferred with NIH funds?  Imagine if libraries only took books supported by rich Europeans.  I am sure Pubmed does this because other agencies don’t pay for the archive but still — I think this is shortsighted.

And today I discovered a new caveat.  A few days ago I used the NIH manuscript submission form to submit author versions of a few of my past papers supported by NIH funds.  And one of them was rejected today because

Your submission to the NIHMS system cannot be processed because the NIH Public Access Policy does not apply to this material. The NIH Public Access Policy does not apply to book chapters, editorials, letters, or conference proceedings. As such, we are sorry that we cannot process your submission.

And though my paper was not one of these things, it is marked in such a way that it seems to be an editorial.  And thus apparently they won’t take it.  I find this a bit surprising since PMC is actually filled with things like editorials including ones by me like PLoS Biology 2.0 and Genomics of Emerging Infectious Disease: A PLoS Collection and meeting reports like Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. 
and letters (none of mine but I found many of others including even responses to letters to the editor). I have run this through my brain over and over and I cannot figure out why (or in fact how) they would exclude these types of materials.   I am going to ask around and see if anyone knows more detail about this but I am not convinced there will be a simple explanation.  Most likely it will have something to do with trying to cover “research” but not opinion.  But in my opinion, research and opinion are not always distinct.

Anyway – I am a bit annoyed by all of this because really, all I want to do is find these best way to share all of my past publications and this seemed like a useful addition to posting them on my website and/or in Mendeley as well as in UC sponsored archives.  And it would be great to have all my papers in PMC.  I note – the vast vast majority of my recent work is in PMC because I basically only publish in Open Access journals that deposit their material there.  But a lot of my old work is not in PMC.  And that is too bad.  Someone, somewhere might find it useful …

——–
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.

——–

New #openaccess journals welcome; competition good; not sure how they know it is "top tier" though

Great news from HHMI, The Wellcome Trust and the Max Planck: http://www.hhmi.org/news/20110627.html

Leading Research Organizations Announce Top-Tier, Open Access Journal for Biomedical and Life Sciences


The Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust announced today that they are to support a new, top-tier, open access journal for biomedical and life sciences research.

The three organizations aim to establish a new journal that will attract and define the very best research publications from across these fields. All research published in the journal will make highly significant contributions that will extend the boundaries of scientific knowledge.

A team of highly regarded, experienced and actively practicing scientists will ensure fair, swift and transparent editorial decisions followed by rapid online publication. The first issue of the journal, whose name has yet to be decided, is expected to be published in the summer of 2012.

The three research organizations developed their plans following a workshop in 2010 at HHMI’s Janelia Farm Research Campus attended by a number of leading scientists. The participants concluded that there was a need for a model of academic publishing that better suits the needs of the research community.

Dr. Robert Tjian, President of the Howard Hughes Medical Institute, says: “The message from the research community was clear: we are fortunate to have many excellent journals, but there is need for a different, more appropriate and efficient publishing model.”

Professor Herbert Jäckle, Vice President of the Max Planck Society, says: “A journal which aims to represent and publish the very best research outcomes needs an editorial team of experienced – and, crucially, actively practicing – scientists. It must also be editorially independent of those who provide the financial support.”

Sir Mark Walport, Director of the Wellcome Trust, says: “We will attract the most outstanding science for publication by establishing a journal in which researchers have confidence in robust editorial decisions taken by their scientific peers. This will be a journal for scientists edited by scientists. The ethos of the journal will be to avoid asking authors to make extensive modifications or perform endless additional experiments before a paper can be published.”

Recruitment is under way for an Editor-in-Chief who – together with the journal’s editorial team – will be an experienced, active scientist. The editorial team will be editorially independent of the funders. They will rely on their scientific expertise and active research experience to identify the best papers, make scientifically-based judgments and exercise leadership in steering these papers through peer review.

The journal will employ an open and transparent peer review process in which papers will be accepted or rejected as rapidly as possible, generally with only one round of revisions, and with limited need for modifications or additional experiments. For transparency, reviewers’ comments will be published anonymously.

As the journal will only exist online, it offers an opportunity to create a journal and article format that will exploit the potential of new technologies to allow for improved data presentation. The journal will be an open access journal, i.e. the entire content will be freely available for all to read, to reproduce and for unrestricted use. This open access system will also enhance opportunities to share content and to more directly engage the reader.

The three organizations have made a commitment to cover costs of launching the journal to ensure its success. The long-term business model will be developed by the incoming Editor-in-Chief and the team they build.

This is great news.  The more #openaccess journals we have the better.  Clearly some of the text here is a dig at existing journals, including PLoS Biology.  PLoS Biology definitely needs to work on some things – like transparency (e.g., if your article is rejected, the Academic Editor who advised the professional editors is not names).  PLoS Biology is also run by professional editors.  Thus it is not run by “active scientists” which is another one of the comments in this press release.  Personally I think it would be better if PLoS Biology was run by active scientists.  But that is not the system there.  I have a strange role at PLoS Biology – “Academic Editor in Chief” for a journal not run by academics.  In essence I am a senior advisor to the professionals who run the journal.  I personally would prefer it if academics ran the journal, probably for the same reasons that HHMI, Wellcome, and Max Planck make such a big deal out of it here.  But the professionals do run PLoS Biology.  And overall, they do a good job.  I think the journal could certainly be better – and thus this new competition should be good.  We will have to wait and see just how much competition it is.  It seems a bit weird for them to call this a “top tier” journal before it exists.  Maybe they should have said “aiming to be a top tier journal” or something like that.  But I think it probably will become one if HHMI and Wellcome and MaxPlanck scientists start publishing their good papers there.  I hope this helps catalyze some beneficial changes at PLoS Biology, but we will have to wait and see.

It is a good time for #OpenAccess when major organizations start to compete to create the best “top tier” open access journal.  In the end, this can only be good for science and scientists. 

——–
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.

——–

Disclosures – we have disclosures – 23&me paper in PLoS Genetics

Well, I must say, this is the first time I have seen something reasonably interesting in the Funding and Competing interests sections of a paper in a while. I saw a tweet about the new Parkinson’s disease paper from 23 & me: PLoS Genetics: Web-Based Genome-Wide Association Study Identifies Two Novel Loci and a Substantial Genetic Component for Parkinson’s Disease

And opening up the paper revealed some interesting material before one even gets to the meat of the paper:

Funding: This study was funded by the participants, by 23andMe, and by a grant from Sergey Brin. Company CEO and co-author AW, wife of SB, has provided financial support to 23andMe for its general operational needs. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: CBD, JYT, ED, AKK, EMD, UF, JLM, AW, and NE are or have been employed by 23andMe and own stock options in the company. 23andMe CEO AW has provided general guidance, including guidance related to the company’s research undertakings and direction. PLoS co-founder Michael B. Eisen is a member of the 23andMe Scientific Advisory Board.

Some fascinating stuff there – and I did know some of it even though my brother, as mentioned above, is a member of the 23 and me Scientific Advisory Board. Interesting that they mention funds from Sergey Brin, stock options, and multiple roles of Anne Wojcicki. Kudos to PLoS for pushing for more disclosures – something we desperately need in science. And Kudos to 23 and me for disclosing the details here and publishing in PLoS Genetics.
Oh, and the paper seems pretty interesting too. But since I do have a bit of a conflict of interest there (with my brother and all) I am not sure I am going to write about the paper itself just yet.
——–
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.

——–

I still love Dropbox – but maybe a little bit less right now

Just got this email

Hi Jonathan,

On June 19, 2011, we had a software bug that caused authentication issues. You can read more about it in our blog post. Our records show that your account wasn’t improperly logged into during this time.

We are writing to you because one or more users you share a Dropbox folder with logged into their account during that period. We have no reason to believe that the login was improper, but in the unlikely event it was, there could have been access to the information in the following shared folder:

  • (Name withheld by me)

We are very sorry as this never should have happened. We are implementing additional safeguards to prevent this from happening again. If you have any questions please contact us at support@dropbox.com

– The Dropbox Team


See The Dropbox Blog » Blog Archive » Yesterday’s Authentication Bug for more detail

——–
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.

——–

Schwag from #synbio5 very popular at home #Amyris #igem

Well, I am missing day 3 of the synthetic biology meeting but I note – I am very popular at home with some of the meeting schwag – thanks Amyris and iGEM

——–
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.

——–

Twisted tree of life award: @Discovermag for article on Lynne Margulis

Well, if you can, for a minute, ignore that fact that in Discover Interview: Lynn Margulis Says She’s Not Controversial, She’s Right | Evolution | DISCOVER Magazine Discover Magazine in essence is promoting some of the refuted ideas Lynne Margulis has about HIV. Sure they hint in part that they think she is over the top but they also give her a soapbox to spout some of her latest absurdities on HIV and such. I would suggest you don’t even read the main part of the Discover article. Just read Tara Smith’s discussion of it: Margulis does it again : Aetiology. Margulis should not be given such prominence in a magazine like Discover. But that is not what I am hear to write about. I am hear to point out that Discover also sets up a red herring for Margulis. In the beginning of the article, it is written:

“A conversation with Lynn Margulis is an effective way to change the way you think about life. Not just your life. All life. Scientists today recognize five groups of life: bacteria, protoctists (amoebas, seaweed), fungi (yeast, mold, mushrooms), plants, and animals. Margulis, a self-described “evolutionist,” makes a convincing case that there are really just two groups, bacteria and everything else.”

Seriously? Scientists today do not recognize five groups. Scientists today have moved past that to recognize and/or argue about bacteria, archaea and eukaryotes – the three domains of life. These three groups were first proposed in 1977 by Carl Woese and colleagues. Did Discover somehow miss the last 34 years of science? WTF? For setting up such an evolutionary red herring in this painful interview with Lynne Margulis, I am giving Discover Mag my coveted “Twisted tree of life award“. Past winners are:

——–
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.

——–

More pics of hand painted poster from #synbio5

——–
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.

——–