Yet another scammy spammy email from the Beverly Hills Times

I get these types of emails from the "Beverly Hills Times Magazine" every once in a while.  They seem spammy or scammy in some way and I thought, rather than suffer alone, maybe I should share.  So here goes:

Fun with Google Books - Old Books on Bacteria

After discovering a copy of this great 100 year old book on "Bacteria in relation to Country Life" on Google Books I decided to snoop around for other old books on bacteria: Microbiology of the Built Environment – as of ~ 100 years ago: Bacteria in relation to country life

The Bacteria by Antoine Magnin in 1880

Bacteria: especially as they are related to the economy of nature by Sir George Newman

Bacteria: their relation to modern medicine, the arts and industries by Frank Bardwell 1891

Bacteria: what they are, what they do, and how they are cultivated by CHarles Marshall 1896

Bacteria: a lecture delivered at the Oamaru Athenæum and ...

Bacteria: or the general study of germs - by Edward McWeeney

Lectures on bacteria - Page 1 - by Anton Bary 1887

If you expand the search to "microbes" you get some other interesting ones

Microbes and the microbe killer

Microbes, ferments and moulds - Page 119

I am sure there are many others that are fascinating there. It is always interesting to me to see what people were thinking about in terms of microbes in the past. And Google Books is one heck of a convenient way to do this.

Rare, not rare, rare, not rare (and this is not about burgers, it's about ocean bacteria)

Nice little press release/story for bacteria and ecology lovers out there: 'Rare' bacteria in the ocean ain't necessarily so, researchers report. This is about work by some colleague of mine including in particular Barbara Campbell at the University of Delaware. I worked with her on a genome project a few years ago (of a bacteria found on the surfaces of some deep sea worms - see Adaptations to submarine hydrothermal environments exemplified ....). Alas, the new paper, in PNAS is not Open Access but the story covers it reasonably well.

Some relevant links:

• Study reported in the July 18 online edition of the Proceedings of the National Academy of Sciences
• U Delaware's College of Earth, Ocean, and Environment
• People | Barbara J. Campbell

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

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

Day 1:  Thursday

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

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

Day 2: Friday: Hanging out at MBL

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

"Yeast in Spaaaaaaaaaaaaaaaaace" - good to have some microbiology on the last Space Shuttle mission

Well, this is a good story lead in

"Chefs across the globe may not know it yet, but their baker's yeast just left the kitchen and blasted off into low Earth orbit".

This is from a NASA press release: NASA - Yeast Rising to the Space Station

Sure - NASA has had some issues with their press released in the recent past. But I like this one. Funny. Interesting. And the science seems, well, worth doing. They are putting the yeast deletion constructs into orbit --- and they are going to use them to study what genes might be involved in survival in microgravity. Sure the connections they try to make to humans are a big big stretch (though I love the "yeastnaut" term), but that didn't bother me for some reason - maybe since it is done in a light hearted way.

Hat tip to Corey Nislow, one of the researchers behind the Yeast in Space project, for pointing me to this story. 

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.

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 ...

A squatter's journey to the Marine Biological Lab (MBL)

Well, I have arrived at the Marine Biological Lab in Woods Hole after a pretty disastrous journal.  I am here to talk in a Symposium that is part of the "Microbial Diversity" summer course: Microbial Diversity - Mbl.edu.  I am hoping all goes better in the next few days than it did yesterday.  I flew from Sacramento to Minneapolis and the plane arrived early.  Then we sat on the runway for 30 or so minutes because first, we did not have an open gate to go to and then second, because the gate staff could not get the walkway to connect to our plane.  Then I thought I was going to barely make my connection to Boston.  Alas, my flight to Boston was delayed due to engine trouble.  I discovered via twitter than some others were also stuck waiting for Delta to fix their planes.

Finally, we boarded and then we sat in the plan for an extra 20 minutes to load luggage and cargo.  Finally I got to Boston - about an hour late - and got picked up by a nice Prius from GoGreenShuttle (thanks Julie Huber for the suggestion) and got to Woods Hole at about 1:30 AM.  I called Lizzie Wilbanks, a Phd student in my lab who is one of the TAs for the course this summer, and she came down with what were supposed to be my keys to one of the dorm rooms in Swope Hall.  She went back to her room and I went to open mine.  Alas, the key did not work.  It was late and I kept trying to get it to work, when a very unhappy woman opened the door and said, in essence "WTF?"  I said, well, this is supposed to be my room.  And she said basically "I don't think so" and shut the door.  Fun.

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. 

Some pics of Ted the Titan Arum "Corpse Flower"

Here are some pics I already posted to twitter of Ted the Titan Arum corpseflower. I took them a few days ago at the UCDavis Botanical Conservancy.

New #ucdavis store open on 2nd street

Pleased to see the new UCD store is open in town

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.

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

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:

• Indoor Air 2011 coming up in Austin, TX – still time to sign up ...
• Reminder – Indoor Air 2011 coming up June 5-10 Austin TX ...
• Indoor Air 2011; Austin, Tx; June 5-10 #microBEnet | Microbiology ...
• The Tree of Life: Off to #IndoorAir 2011 in Austin, TX - to ...

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.

• Sacramento to Las Vegas to Austin to #IndoorAir2011#fb

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.

A great moment for plant sciences: winners of HHMI-GBMF competition for Plant Science Program Investigators announced

This is truly the golden era for plant sciences. One key sign of this is the announcement of the winners of the competition to become HHMI Investigators in Plant Sciences.

HHMI, the Howard Hughes Medical Institute, has for many years picked HHMI Investigators in Biomedical Research. Those picked get guaranteed funds for 5 years and become technically employees of HHMI in order to get them out of miscellaneous burdensome university activities. It's a win win situation for universities because HHMI pays for space and salaries for the Investigators. I myself tried to get me one of these "Uncle Howie" types of positions a few years ago but did not win out. My brother, Michael, did. The other people they picked the year they picked Michael and not me were all very good, so I actually did not feel so bad about not getting it.

HHMI has also invested in other areas related to biomedical research including funding Janelia Farm, and Early Career Scientist program, as well as many educational activities.

The GBMF, aka the Gordon and Betty Moore Foundation has itself made major contributions to science and medicine in various ways. One example is the Marine Microbiology Initiative (MMI) (which funded the iSEEM project for which I am PI) and cool work out of many top marine labs. In fact, the MMI program did something rarely seen outside of HHMI - they funded "people not projects" by creating MMI Investigators who got a good chunk of money to do pretty much whatever they wanted.

Thus it was great to hear some time ago that GBMF and HHMI were coming together to create a Plant Sciences Investigator program. I confess even though I am not a real plant biologist I considered applying for this because I have shifted much of my work recently into studies of plant associated microbiomes. But I did not apply. And I kept wondering - who would emerge from the competition as winners. Would they be people I respected/had heard of?

Well the wait is over. Last week the winners were announced: HHMI News: 2011 Plant Science Program HHMI-GBMF Investigators. And it is quite an incredible crew. The press release from HHMI-GBMF is quite useful (unlike many press releases in the sciences). Here is a list of the winners with some additional details (taken from the HHMI site - I hope they do not mind).

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:

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

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:

• Twisted Tree of Life Award #9: Nature News on the "Marsupial" platypus
• Twisted Tree of Life Award #7 #8: Alroy on "Changing the rules of evolution"
• Twisted Tree of Life Award: NPR on the Evolution of Crying
• Twisted tree of life award #6: Scientific American Origins piece for dissing microbes
• Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc
• Twisted Tree of Life Award #4: Hoxful Monsters Blog on "Primitive" Animals
• Twisted Tree of Life Award #3: The Columbus Dispatch on Ancient Bacteria
• Twisted Tree of Life Award #2: Science Friday on the Five Kingdoms
• Twisted Tree of Life Award #1: Salk Institute Press Release on Kinases

More pics of hand painted poster from #synbio5

More art & science - hand painted poster at Synthetic Biology #synbio5 - by Karmella Haynes

I posted this to twitter yesterday but am now adding it to my blog since it was so great.  At the Synthetic Biology 5.0 meeting at Stanford I walked into the poster session last night to discover this incredible poster:

Karmella Haynes, had hand painted her poster on canvas.  Drawn in by the art, I went to talk to her (well, first I said "This is awesome" or something like that.  And then I found out a bit more detail.  She had her paints with her and was continuing to add touches to the painting.  Though I was fascinated by the art side of this, then we got to talking about the science because actually - the figures there were about work she had done on applying some ideas from synthetic biology to animal cells in tissue culture.

I was completely blown away by this.  I am not sure if the same posters will be up tomorrow and if so I will try to get some better shots.  Anyway, I found out she is on her way to a faculty position in Arizona and has recently been a post doctoral fellow at Davidson College.

And then with a little help from Google I discovered her openwetware page: Karmella Haynes.  And from that I found her art page: http://www.karmellahaynes.com/.  I hope she does more hand painted posters for conferences - it certainly brightened up the poster session and made my day.

Absolutely spectacular - glass microbes

Wow. These are truly spectacular: Gallery – Glass Microbiology - Luke Jerram

Thanks to Morgan Jackson for pointing me to them via twitter: here

See also:

• A Rare Collection of Victorian Glass Microbes
• Glass Microbes, Science Goes Stylish | A Schooner of Science
• 
  

Coming up on http://phyloseminar.org Jason Stajich (aka @hyphaltip) #fungi #genomics

Upcoming seminar on Phyloseminar.Org

Jason Stajich speaks Wednesday, June 29th at noon PST on "Fungal phylogenomics: Getting lost in the moldy forest."
Fungi occupy diverse ecological niches in roles from nutrient cycling in rainforest floors to aggressive plant and animal pathogens. Molecular phylogenetics has helped resolve many of branches on the Fungal tree of life and enabling studies of evolution across this diverse kingdom. The genome sequences from hundreds of fungi now permit the study of change in genes and gene content in this phylogenetic context and to connect molecular evolution with adaptation to ecological niches or changes in lifestyles. I will describe our work in studies contrasting pathogenic and non-pathogenic fungi and efforts to unravel the evolution of multicellularity in fungi comparing unicellular basal fungi with multicellular mushrooms and molds.
The development of tools for data mining and use of fungal genomics is also driving the pace of molecular biology and genetics of fungi. I will highlight new approaches to make this easier and the ways data integration can inform and transform studies of functional biology of fungi.

Japan	04:00 (04:00 AM) on Thursday, June 30
New Zealand	07:00 (07:00 AM) on Thursday, June 30
West Coast USA	12:00 (12:00 PM) on Wednesday, June 29
East Coast USA	15:00 (03:00 PM) on Wednesday, June 29
England	20:00 (08:00 PM) on Wednesday, June 29
France	21:00 (09:00 PM) on Wednesday, June 29

Learn how to connect ahead of time. To hear about upcoming talks, send an email to phyloseminar+subscribe@googlegroups.com or follow @ematsen.
If you can't make it, don't fret-- you can always watch the recording

Yes, I am a #RedSox & #PLoS fan; & this video sort of is proof #BenFranklinAward #OpenScience

Just saw this posted on Youtube.  Did not know it was coming ... but am happy they recorded it



And here are the slides I used.  Will try to synch

Ben Franklin Award Slides

View more presentations from Jonathan Eisen

For more on this award see

• UC Davis' Jonathan Eisen Wins 2011 Benjamin Franklin Award - Bio ...
• Back in Boston, Eisen Celebrates 2011 Benjamin Franklin Award ...
• BioMed Central Blog : Jonathan Eisen: 2011 Benjamin Franklin Laureate
• Boston, Bioinformatics & Ben Franklin Award wrap up from #BioIT11

How about this? Wash your hands. Please. (Nice video from SLV Health)

Saw this news story a while ago: Videos help spread word of bacteria, other health issues | Deseret News but only just got to watching the video from Salt Lake Valley Health. 



I note - my post originally said "Wash you hands" and my 6 year old daughter was snooping at my computer and said "Daddy, it says 'wash you hands' not 'wash your hands.'" Well, I think I found a new blog editor.

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.

Fun with Ligercat: pubmed word clouds

I have been having enormous fun over the last hour playing with LigerCat.  I was searching for ways to build tag clouds for papers in Pubmed and this came up: LigerCat: Using “MeSH Clouds” from Journal, Article, or Gene Citations to Facilitate the Identification of Relevant Biomedical Literature.   And they have a web site to do searches: LigerCat Literature and Genomics Resource Catalogue

So, of course, like many others, the first thing I did was search for myself:

Eisen JA

Quick update (pics, twitter feed) on #IndoorAir2011 in Austin, TX #microBEnet

Here are some pics from my trip to the Indoor Air 2011 meeting. I am going to post more detail about the meeting later.



If you want some information about what happened at the meeting, best place right now is probably twitter




Also see the microBEnet blog which has some recent posts on this.

Worst new omicsword, perhaps ever, the Dispensome #awful #badomics #reallybad #uggh

Well, I do not even have any idea what to say. I got pointed to this paper: PLoS Genetics: Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis by KamounLab on twitter. The authors of the paper include colleagues at the DOE-Joint Genome Institute so it is possible that they are baiting me to get some attention. But YHGTBFKM - the dispensome? Defined by them as "The dispensable chromosomes collectively comprise the dispensome and showed extreme plasticity during sexual reproduction." Now, I have seen my share of bad omics words (and which I write about often with, for example, my Worst New Omics Word Award and Bad Omics Word of the Day). But this is the first case where the word, and the excessive use of it in the paper is distracting (as suggested by KamounLab) to the science. Is this word really necessary? Could they not just say "dispensable chromosomes" (which I note, I might still have problems with since they would only be known as dispensable under certain conditions)? But "dispensome" is unnecessary, distracting, and, well, not a good word. Thus in this case I have decided to not even give them an award per se but to simply say that I think this is possibly the worst omics word I have ever seen. I note - I am not criticizing the science (nor endorsing it mind you) they did here. But the word, oh the word. It hurts me. It really does.

I like this pic of me so much it gets a whole post - "Apple Love" by Rhonda Roman

Apple Love by Rhonda Roman

 So a few Saturday's ago I was at the Davis Farmer's Market and Steve Smit from Mt. Moriah Farm's showed me this pic that a photographer had given him.  Steve is one of my favorite people anywhere.  I don't know why really.  But I go to the Farmer's Market many times just to see him/buy stuff from him.  He is funny, warm, interesting, social, etc.  And apparently a photographer caught one of our interactions from earlier this year.  

Fortunately, she put her name on the back of the picture and a little googling and I found her photo collection on flickr.  Her name is Rhonda Roman and I really like her collections there.  But in particular I love this picture she took of me and Steven and others at the Market.  It captures everything really about my interactions with Steve.  Thanks Rhonda.  A picture is worth way way more than 1000 words.

#UCDavis to partner with the Beijing Genome Institute (BGI)

Well, it is now formal so I guess I can post about it here.  UC Davis is officially developing a genomics partnership with the Beijing Genomics Institute (BGI).

For more on this breaking news see

• Chinese genomics giant BGI and UC Davis form partnership (Eurekalert)
• CHINESE GENOMICS GIANT BGI AND UC DAVIS FORM ... (BGI web site)
• Chinese Genomics Giant BGI and UC Davis Form Partnership

Not much detail there I know - but in essence the plan is to build a partnership between UC Davis and BGI with BGI provided genomics and informatics expertise and capabilities and Davis providing biological expertise and diversity (of course, Davis has some genomics chops too and BGI does some biology but you probably get the point). 

For those who do not know, BGI is a relative newcomer on the block in terms of large scale genomics research institutes.  But by being new they have had a massive advantage in a way in that they are really the first to be developed as a "Second-generation Genome Center" having been built / developed with the new second generation sequencing systems at its core.  Thus while other large centers around the world have tried to adapt to the new second generation sequencing systems, BGI started from scratch and could build it's enterprise around the new systems.  

I am excited about the possible connections with BGI though I confess I do not know a whole lot about the plans.  There have been lots of whisperings here at Davis about building a partnership with BGI and people have been a bit nervous about word getting out too early.  So, though I have heard some details I have not been an active part of the discussions.  However, whatever the plans are I am looking forward to interactions with BGI.  They are really pushing the frontiers of genome sequencing in many ways.  And despite the moans and groans from many people, I do not think genome sequencing is on a downward slope in any way.  For example, as a tool in studying microbes, genome sequencing still has many many years of use - after all there are hundreds of millions of microbial species that have yet to be studied and each one has lots of intraspecific diversity (e.g., across geography) to be characterized.  

And as a UC Davis faculty member I think BGI picked a great place to work with.  Davis has an almost unprecedented diversity of faculty working on some area in the life sciences - and these faculty come from across campus from the College of Biological Sciences, School of Medicine, Viticulture and Enology, School of Veterinary Medicine, College of Agriculture and Environmental Sciences, College of Engineering, School of Nursing, and College of Letters and Sciences.  In fact, you could say - in a way - UC Davis is a campus more dedicated to Life Sciences than almost any other place in the world.  

This development is just one of many that make me impressed with the new UC Davis Administration.    Ever since Chancellor Katehi came on board I have been pleased with almost every major initiative and development and administrative hire on campus.  Sure - the budget cuts from the California government hurt.  But in challenging times, you need great leadership.  And we certainly have it at UC Davis these days.  And if you think I am just sucking up, you should read some of the things I wrote about our previous administration.  I really am impressed here.  

I do not know what will happen with the BGI - UC Davis partnership.  Right now it is just a plan.  But I will do what I can to help it succeed and I am looking forward to interactions with BGI and the bright future at UC Davis. 

Off to #IndoorAir 2011 in Austin, TX - to discuss and promote http://microbe.net #microBEnet

Well, off to Austin for a meeting I would not have imagined going to a few years ago. Indoor Air 2011. Why am I going? Because a few years ago I began to discuss studying the microbiology of the built environment with Paula Olsiewski, from the Alfred P. Sloan Foundation. You see, the Sloan Foundation has a new program in this area "The Indoor Environment". Eventually, after much discussion I applied for a grant in their program. My grant is a bit unusual (for me and for others probably) in that it focuses on communication, coordination, networking, collaboration, etc.

My project is called "microBEnet" - which stands for "microbiology of the Built Environment network". The BE is purposefully capitalized to emphasize the Built Environment part and we figure, since microbes are small, the m should be lower case. For more on the project see: Microbiology of the Built Environment Network | Site for the microBEnet project. As part of this project, a collaborator (Hal Levin) and I are doing many activities and I will post more about them over time. Among our activities are a new blog, and a diversity of resources.

Which brings me to Indoor Air 2011.  We are also starting to organize or help organize some meetings and workshops to bring together the various folks who might be interested in microbiology of the built environment.  And for Indoor Air we have helped the meeting organizer Rich Corsi plan some sessions on microbiology of the built environment.  The sessions take place Wednesday and Thursday and should be great.   Looking forward to going to Austin, maybe seeing some friends at UT and nearby (hint hint Dr. Hillis, Sheril K, etc) and learning about the built environment.

Apparently, my own local paper hates my blog

I mean, I knew evolution was controversial and that I can be a bit snarky at times.  But does my own local paper -the Davis Enterprise have to have a whole article about how they hate me and my blog?

Crosspost from http://microBE.net: New, massive volumes on #metagenomics coming out soon

For those interested in microbial diversity and/or metagenomics there are two volumes that are coming out soon that are of interest:

• Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches.
• Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats

Edited by Frans J. de Bruijn these two volumes are the most comprehensive coverage of metagenomics out there right now. The chapters are almost overwhelming (full disclosure, I have two chapters in here - both of which are republications of Open Access papers I have published on metagenomics).  See below for full chapter lists.

Order from Amazon:

• Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches
• Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats
• Handbook of Molecular Microbial Ecology, Set

Sequence/short read archive (SRA) back from the dead

Well, in February it seemed as though the Sequence/Short Read Archive was dead (see for example, End of Sequence Read Archive (SRA) - some quick notes and Though I generally love NCBI, the Sequence/Short Read Archive (SRA) seems to have issues; what do others think?)).

But now it seems as though there has been a resurrection of sorts (I guess I should have paid attention in March). See for example: SRA Home where it is stated that

"Recently, NCBI announced that due to budget constraints, it would be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. However, NIH has since committed interim funding for SRA in its current form until October 1, 2011. In addition, NCBI has been working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next generation sequencing data after October 1, 2011.

We now plan to continue handling sequencing data associated with:

RNA-Seq, ChIP-Seq, and epigenomic data that are submitted to GEO

Genomic and Transcriptomic assemblies that are submitted to GenBank

Genomic assemblies to GenBank/WGS

16S ribosomal RNA data associated with metagenomics that are submitted to GenBank

In addition, NCBI will continue to provide access to existing SRA and Trace Archive data for the foreseeable future. NCBI is also continuing to discuss with NIH Institutes approaches for handling other next-generation sequencing data associated with specific large-scale studies."

Well I'll be. I guess it is back at least for now.

New #UCDavis Dean of the College of Biological Sciences: James E.K. Hildreth

Just announced a few minutes ago. The new Dean of the College of Biological Sciences at UC Davis is James Hildreth from Meharry Medical College.

Some tidbits about him:

• Harvard College, cum laude in Chemistry
• Rhodes Scholar
• PhD in Immunology from Oxford (I think)
• MD from Johns Hopkins
• Many major discoveries related to HIV. See for example:
• Evidence for budding of human immunodeficiency virus type 1 selectively from glycolipid-enriched membrane lipid rafts
• The Trojan exosome hypothesis

Selfish DNA, symbionts and parasites - some quick links

I was at a committee meeting yesterday for a great PhD student here at UC Davis, Michael Hornsby and the topic of selfish DNA came up.  After his meeting we sat down and looked for some new papers and review papers on the topic.  I just thought it might be of value to share some of these here:

• The Myth … of the Myth of Junk DNA (blog post by John Farrell)
• A formal theory of the selfish gene
• Capturing the superorganism: a formal theory of group adaptation.
• Bacterial toxin-antitoxin systems: more than selfish entities?
• Genomic islands: tools of bacterial horizontal gene transfer and evolution.
• A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution
• What traits are carried on mobile genetic elements, and why?

We also discussed briefly the evolution of mutualists and parasites and here are a few papers that came up:

• Genomics and evolution of heritable bacterial symbionts.
• From parasite to mutualist: rapid evolution of Wolbachia in natural populations of Drosophila.

If anyone knows of any other good recent papers or blog posts about selfish DNA or mutualists vs. parasites please post them here.  Thanks

NSF requests for "conflicts of interest" lists drive me batty and seem to penalize collaborative, interdisciplinary researchers

OK, time to bitch and moan a bit.

I am working on a few proposals to the National Science Foundation where NSF asks one to include "lists of institutions, project personnel, and collaborators with Conflicts of Interest".

Seems simple I suppose.  But not when you get down to the details.  For example I found some guidance from the NSF about this where they ask one to list coauthors, collaborators, co-editors, students, advisors, advisees, friends, relatives, and many other affiliations.

To make a very long story short.  NSF wants you to make a list of anyone who possibly should not review your grant.  And if you are involved in many large collaborative projects or teach or train a lot of students.  Well, you are screwed.  For example, if they really want me to be thorough, I would probably have to list more than 500 people.  This would include a few hundred co-authors and hundreds of collaborators (e.g., on some projects I am working on with the Joint Genome Institute there are hundreds of people involved in some way).

What's Lurking in Your (Work) Basement

Well, sad as it may be I finally made it into the basement in the building where I have worked for five + years - the Genome and Biomedical Sciences Facility (GBSF) at UC Davis (the Genome Center is in the same building).  There, down in the basement they were having an Open House for the CMGI - the Center for Molecular and Genomic Imaging.  I knew of some of the stuff they did but had never been down to see their facility and their, well, toys.  And it was really cool.



They also had a nice food spread upstairs on the first floor of our building that I discovered later.  The best part of this spread were the animal chocolates and carvings:

A good day for the Public Library of Science and science in general: #PLoS opens up search API

Well, thanks to @yokofakun (Pierre Lindenbaum) and #gepasi (Pedro Mendes) on twitter I found out about the announcement from the Public Library of Science (PLoS) yesterday that they have opened up a search application programming interface (API) to allow outside users better access to PLoS searching (see the PLoS blog: PLoS API). This is a great step for PLoS and should accelerate the ways that people access and search for content at PLoS. For more information see:

• Announcing the PLoS Search API – build innovative applications that accelerate science
• Fields in the PLoS Search engine
• some examples using the PLoS API
• PLoS API developers group

To use it you need to register for an PLoS API Key (I just got one, not that I will use it, but was just checking ...). 

Looking forward to seeing what people do with this.

Crosspost from microBEnet: Where is metagenomic analysis heading? Hopefully in directions suggested in this paper.

Figure 3 from Raes et al. Molecular Systems Biology 7 #473  doi:10.1038/msb.2011.6 

Just a quick post here.  I have been reading this paper: Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data by Jeroen Raes et al. in Molecular Systems Biology.  This integration they try to pull off in the paper is to me where we need to move as a field (i.e., microbial ecology) in order to make full use of metagenomic data.  The paper provides a nice overview of microbial biogeography too.  Definitely worth a read.

Am crossposting this from the microBEnet blog (microBEnet is the site for the microbiology of the built environment network that I am building):