Notes from my trip to #AAASMtg #EarthMicrobiomeProject #Storify

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

Slideshow version of Storification

Slideshow w/ audio of my talk on "A Field Guide to the Microbes" from the AAAS Meeting #AAASMtg

I recorded the audio of my talk on "Towards a field guide to the microbes" from the AAAS meeting on Saturday AM. Here is a slideshow of the talk with audio synched to the slides (I did this using Keynote on a Mac with the "record Slideshow" function).





My slides from the talk are available at Slideshare.

Jack Gilbert @gilbertjacka clarifies comments at #AAASMtg re: opening windows, cleanliness & microbes

Just got this to post from my college colleague Jack Gilbert in regard to some comments he made to the press at the AAAS Meeting a few days ago.  He sent this in part in response to some news stories that came out of the press conference we had at the meeting (e.g., see Florence Nightingale approach 'could help fight infection in ..., Open hospital windows to stem spread of infections, says ... and others).  And I encouraged him to consider whether or not he needed to clarify some of his comments - and here is his response.

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A confession, lesson and retraction
By Jack A. Gilbert

At the AAAS 2012 annual meeting on Friday, I was involved in a press conference to announce the initial results and ideology for the Earth Microbiome Project (http://www.earthmicrobiome.org). Following the press conference we went to another room, where we were openly discussing these concepts with the reporters. Several reporters asked me to comment on the potential impact of this research in the medical sphere. At which point I started to discuss some excellent research by Jessica Green (http://biology.uoregon.edu/people/green) regarding her recent evidence that improved ventilation in hospital wards reduced the airborne abundance of organisms that were related to pathogens. I showed these reporters the paper
(http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2011211a.html) and asked them to discuss this with Jessica Green.

I then proceeded to discuss some current research we are doing at University of Chicago that is looking at the impact of having a natural microbial community on surfaces to reduce the likelihood that pathogens can establish in that environment. Specifically we are exploring whether 'good bacteria' can be used as a barrier to outcompete 'bad bacteria', I suggested that this was testing the hypothesis outlined by Florence Nightingale.

To this end I said, that maybe instead of sterilizing every surface in a hospital we could explore a different strategy. There is however currently only circumstantial evidence to support my claims, and I could have done a much better job in making clear that I was discussing an idea - not something for which there was evidence.

I am sorry for my indiscretion and hyperbole, and hope that I didn't cause any groups or individuals concern or worry about this topic. These were concepts being discussed, specifically that by using the EMP we could explore ecological dynamics that could lay the groundwork to help determine if a community could play the role of a barrier against infection.

I want to stipulate that I believe hospitals should be cleaning, and I believe that surgeons should scrub and use the sterile method. To be clear, I wanted to state that 'good' bacteria could in the future play a role in reducing the instances of hospital borne infection, and that this is something we should investigate. People should wash their hands after the toilet, and wash their hands when they are sick; there is nothing wrong with being clean.

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

Calling on AAAS to Deposit all Archives of Science in Pubmed Central

Much has been written recently about a call to boycott Elsevier due to their outrageous policies regarding academic publishing.  I support the boycott but I also agree with many others who have said it perhaps unnecessarily singles out one publisher over others who also have publishing policies that could, well, use a bit of work.  And one such publisher is AAAS - the American Association for the Advancement of Science.

Today, the annual meeting of AAAS begins today in Vancouver.  I was supposed to be there by now, but thanks to some technical problems at Alaska Airlines, I am back in Davis for the day.  AAAS has some policies regarding openness that I believe are unnecessary and not in the general interest of scientific progress.  One is the strange "talk embargoes" I have written about recently.  Another, which is much more problematic, is the fact that Science Magazine (published by AAAS) does not deposit archival content in Pubmed Central.  Now, mind you, I think all scientific publishing funded by taxpayer money should be openly and freely available immediately. But that is not going to happen immediately.

One helpful tool in making scientific literature freely available is Pubmed Central.  Most scientific societies I know of deposit published material in Pubmed Central after some initial delay of 3-6-12 months.  But for reasons that are not entirely clear (to me at least, or to a Google search), AAAS clings to their archival material making it only available through their own web site.  Sure - they do allow authors to deposit their version of their manuscripts in Pubmed Central after a delay.  But most alas do not do this.  And I note - this option is only open to NIH and Wellcome Trust funded work.  So much material cannot be deposited anyway.

AAAS's policy seems unnecessarily closed accessy and limits the impact and spread of the knowledge contained within papers in Science.  I note - this policy is yet another reason to not publish in Science and to instead choose either fully open access journals or ones that at least release their stranglehold on the papers after a short delay.

Today I call on AAAS to make archival literature from Science Magazine available in Pubmed Central.  And I call on others out there, such as those at the AAAS meeting, to pressure AAAS to do this.  Write blog posts.  Call and email AAAS members and leadership.  Email AAAS.  And so on.

Ideally everyone would just publish in fully open access journals and the journals would deposit material in archives.  But until that happens, we need to make every effort to increase the amount of literature getting into Pubmed Central and other archives.  So - pressure AAAS.  And while everyone is at it, please deposit whatever you can in preprint servers, in various repositories and in Pubmed Central.  Every little bit helps.

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

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

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


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



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


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


Your individual username and password for the site:


Please provide the following:


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


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


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


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


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


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


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

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

To whom it may concern


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


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


Sincerely


Jonathan Eisen

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

AAAS meeting - is this one for embargo watch?

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

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



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

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

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

Dear AAAS Annual Meeting Participant:

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

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

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

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

Your individual username and password for the site:

Username: xxxx
Password: xxxx

Please provide the following:

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

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

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

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

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

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

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

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