No Ovaries? Well this Ovarian Club Conference is For You (YAMMMs for everyone)

Well, I just got an email invitation to attend CME - OVARIAN CLUB 4.  And alas, rather than just dumping it into SPAM (which I did do) I clicked on one of the links.  I had to know - what was the gender balance at this meeting.  Was there any chance that the organizers would see that it would be ironic to not have a decent number of female speakers?  Alas, nope.

The organizing committee is 17:1 males to females.

And the speaker balance is not much better something like 25:6.




I guess maybe they should rename this "Meeting brought to you by people who mostly do not have ovaries."  Sad.  Another YAMMM (Yet another mostly male meeting).



Related posts and pages

No #AAAS and ASM you do not deserve good PR for freeing up a few papers on Ebola

Saw a PR from AAAS about how they were freeing up all of ~ 20 papers on Ebola
In light of what has become the largest Ebola outbreak on record, Science and Science Translational Medicine have compiled over a decade's worth of their published news and research. Researchers and the general public can now view this special collection for free.
OK. More access is good. But alas, they did not even free up all papers in #AAAS journals with Ebola in the Title or Abstract.

And then I started thinking. What about HIV? TB? Malaria? And as I started Tweeting about this, I saw that ASM also was hopping on the "free Ebola" bandwagon (actually I do not know who did it first).

Today's YAMMM (Yet another mostly male meeting): pharma-nutrition #PN2015

Just got pointed to (by Elisabeth Bik) an announcement for a meeting: Home : Pharma-Nutrition 2015 with a focus on "Linking the Microbiome with Nutrition and Pharma".  And alas, the list of confirmed speakers is as follows:
  • Keynote Speaker
    • Martin J. Blaser, NY University Medical Center, New York, NY, USA
  • Speakers
    • Gregor Reid, University of Western Ontario, London, ON, Canada 
    • Alain van Gool, Radboud University, Nijmegen, The Netherlands 
    • David Hafler, Yale, New Haven, CT, USA 
    • John F. Cryan, University College Cork, Cork, Ireland 
    • André Marette, Laval University, Montreal, QC, Canada 
    • Charles R. Mackay, Monash University, Clayton, Victoria, Australia
    • Alan L. Landay, Rush University Medical Center, Chicago, IL, USA
Yay.  All men.  How wonderful.  Because, you know, there are no women working on the microbiome and nutrition right?  Ugg.

Seems like they are still working on getting more speakers.  I will send this blog post to the organizers and see what they say.  But suffice it to say I am very disappointed in them.  Oh, and shockingly, the two organizers are men: Johan Garssen and Alan Landay.

These YAMMMs (Yet Another Mostly Male Meeting) really have got to be killed.  People should not got to them.  People should not speak at them.  And the organizers should not be allowed to run other meetings unless they can explain themselves and provide evidence that they will work to not have this happen again.


UPDATE A FEW MINUTES AFTER POSTING.

I found the program committee for the meeting.  Alas the gender ratio there is lame too.
  • John F Cryan, University College Cork, Cork, Ireland
  • Alain van Gool, Radboud University Medical Centre, Nijmegen, The Netherlands
  • David Hafler, Yale School of Medicine, New Haven, CT, USA
  • Charles R Mackay, Monash University, Melbourne, Australia
  • André Marette, Laval University, Sainte-Foy, QC, Canada
  • Gregor Reid, Lawson Health Research Institute, London, ON, Canada
And a bit strangely - all of the people on the program committee are speakers.  No bias there.

Nice Art and Science example - UC Davis Medical School molecule sculpture

Quikc post here.  A month or so ago I went to the UC Davis Medical School in Sacramento for a meeting and got to see this amazing new sculpture for the first time.




For more about this and the Artist Roger Berry see this article.  It is always inspiring and uplifting to see nice architecture and nice art in a science building. 


AAAS - Blocking Access to the Scientific Literature Even When They Say It Is "Free"

Today, I wanted to show someone a PDF of a paper of mine that I co-authored in 1999.  The paper was, I think, kind of cool.  It reported the sequencing and analysis of the genome of Deinococcus radiodurans, an incredibly radiation resistant bacterium.  Alas, I did not have a copy on me, and the only electornic device I had with me was my phone.  The person I wanted to show the paper to had their computer, a device with a strange little red trackball and running some sort of Windows operating system, so I looked at it and panicked and said "Maybe you should drive" (as in, maybe they should be the one controlling the computer).

So this person, who shall remain anonymous mostly because of the ancientness of their computer, did the kind of obvious thing, and opened a web browser (don't even ask which one) and typed in "Pubmed.Com".  OK - that would work.  I might have preferred going to Google Scholar, but I use Pubmed about as frequently.  And though I do not have a Windows machine or the weird web broswser they used, I have recreated what happened next.


A nice Pubmed window.  And I said, type in "Deinococcus Eisen." and seven papers showed up.





AAAS and SnapChat collaborate to develop SnapScience to publish scientific papers transiently

Just got this in an email and thought it should be shared.

Washington, DC. August 15, 2014.

Kent Anderson, the newly appointed Publisher of AAAS (see http://www.aaas.org/news/aaas-names-new-science-publisher) has announced his first action as Publisher - a partnership between AAAS and Snapchat (https://www.snapchat.com).

Anderson said "Although I will not officially assume the role of Science publisher until 3 November, this was too important a task to not carry out immediately. AAAS has always been looking for new ways to reduce the public availability of scientific publications. AAAS approached Snapchat a few months ago and in secret developed a new App "SnapScience" which allows the transient publication of scientific articles. Article longevity can be set to 1 minute, 5 minutes or 15 minutes."

Anderson followed this with "This kind of thing I had always hoped to do in my role as president of the Society for Scholarly Publishing but the technology was just not available. Snapchat has developed the perfect platform for the future of AAAS and scholarly publishing in general with its ability to allow readers a glimpse of a scientific article but not allow them to keep it or reread it or redisplay it."

AAAS CEO Phil Lesher said "We have had serious issues recently with the public demanding access to articles in Science and other AAAS published journals. And in addition, we have published a slew of papers that have needed to be retracted shortly after publication. This solves both issues. First, all papers will only be transiently available, so their there is no need for retractions. Second, even scientists will only have short term access to papers so the public cannot possibly demand access for themselves."

Anderson also said "We think SnapScience is the perfect way for me to step into my new role as Publisher of the Science family of journals. It is cutting edge. It is exactly the type of thing that publishers have been looking for. And it will be fun."

AAAS hopes to roll out updates to SnapScience that will allow researchers to also publish data and protocols only transiently as well.

Today's YAMMM (Yet Another Mostly Male Meeting) Brought to You by CIFAR & NAS

Well, just got an invite to this meeting: Symbioses becoming permanent: The origins and evolutionary trajectories of organelles.  The topic seems of direct interest to what I work on.  And, it is relatively close (Irvine is a short hop away).  So this could be a way to go to a meeting without having to travel too far.  And maybe I could see my younger brother Matt who lives in LA and just graduated from UC Irvine's Masters program in Sound Engineering. Then I looked at the schedule of speakers and organizers.  Many are friends.  Many others are colleagues.  Could be fun to see some people I have not seen in a while.  And then I realized, most - no nearly all of them - are men.  Below I list the people involved in the meeting, highlighting men in yellow and women in blue.

Organizers: W. Ford Doolittle, Patrick Keeling, and John McCutcheon

Distinctive Voices Public Lecture presented by Michael Gray, CIFAR Advisor, Dalhousie University

Session 1: Genomes (evolutionary rates, oddities, and reduction)
  • Introduction and welcome remarks – W. Ford Doolittle, CIFAR Advisor & Patrick Keeling, CIFAR Program Director and Senior Fellow
  • John McCutcheon, CIFAR Associate Fellow, University of Montana
  • John Archibald, CIFAR Senior Fellow, Dalhousie University, Nuclear organelles 
  • Andrew Roger, CIFAR Senior Fellow, Dalhousie University, Organelle reduction 
  • Siv Andersson, Uppsala University, Alphaproteobacterial genome evolution 
  • David Smith, University of Western Ontario, Roots of genomic architecture variation 
  • Daniel Sloan, Colorado State University, Cytonuclear co-evolution under extreme mitochondrial mutation rates
  • John Allen, University College London, Why keep genomes?
Session 2: Integration/Control (trafficking, signaling, transporters)
  • Debash Bhattacharya, Rutgers University, Transporters in organellogenesis 
  • Nancy Moran, University of Texas, Austin, Insect endosymbionts 
  • Geoff McFadden, University of Melbourne, Diversity of protein trafficking
  • Chris Howe, Cambridge University, Why integrate?
  • Steve Perlman, CIFAR Fellow, University of Victoria, Maternal transmission, sex ratio distortion, and mitochondria 
  • William Martin, Düsseldorf University, Endosymbiont and organelle, what’s the difference? 
  • Moriya Okhuma, Riken University, Metabolic integration across endosymbiotic communities
Session 3: Theories and Models
  • Eors Szathmary, Loránd University, A fresh look at cooperation in some major transitions, especially the origin of eukaryotes
  • Marc Ereshefsky, University of Calgary, Evolutionary individuality
  • Peter Godfrey-Smith, City University of New York, Individuality and the egalitarian transitions 
  • Maureen O’Malley, University of Sydney, Philosophical Reflections on Endosymbiosis: Implications for Evolutionary Theory
  • Toby Kiers, University Amsterdam, Bacterial cooperativity
Closing remarks J. McCutcheon


So - that appears to be a ratio of 18 male speakers and 4 female speakers for a whopping 18% female speakers.  No thanks CIFAR and NAS.  I will sign up for a different meeting.  And by the way - WTF?  There are so so many qualified women working on these topics - what let to this 18:4 ratio?  The organizers should really rethink their processes and the sponsors should pull funding from meetings like this.  It is the only way some people will pay attention to diversity.


UPDATE: 8/20

Wrote to the NAS via their Website

To whom it may concern:

I am writing to express my disappointment in the gender ratio of speakers at this meeting (18 males, 4 females).  Due to the skew I am unwilling to participate.  See http://phylogenomics.blogspot.com/2014/08/todays-yammm-yet-another-mostly-male.html for details.

Sincerely,

Jonathan Eisen
Got this response

Dear Dr. Eisen,

The NAS Committee on Scientific Programs, which oversees the Sackler Colloquia most definitely considers gender diversity when approving these programs.  When organizers propose the programs they achieve a good balance on paper. Regrettably, in many fields, women scientists are at a premium and are sometimes overwhelmed with invitations and demands for their participation on programs and committees.  For a variety of reasons, including availability of speakers, the final program is not always as optimally balanced as originally intended.

I have conveyed your message to NAS Vice President and Chair of the Committee on Scientific Programs and will also share your concerns with the colloquium organizers and co-sponsor.

Best regards,

Susan Marty
Program Director
National Academy of Sciences
Sackler Colloquia
http://www.nasonline.org/programs/sackler-colloquia/

So I wrote back

Susan 
Thank you very much for the response.  It is good to hear there is some emphasis on gender diversity when programs and developed.  However, in my experience and based on my readings of the literature on this topic, this is not usually sufficient to produce diverse conferences.  Do you know if the NAS has any additional policies relating to diversity at conferences.  For example, if someone does not accept an invitation, is the organizer of the meeting then free to select whomever they like or are there protocols to help guarantee that the selection of replacements is also diverse?  Also do you know if there are any policies relating to the meetings themselves such as child care that have been shown to impact the attendance of women more than men?   
Any additional information you have would be appreciated.  I think that NAS could and should do more than just review the proposed list of invitees. 
Sincerely
Jonathan Eisen 

An important read: Emma Pierson on gender and authorship position in science

This is a fascinating read: In Science, It Matters That Women Come Last | FiveThirtyEight.  By Emma Pierson, who works at 23 and me.  It has all sorts of references of use and details on authorship position in scientific publications and how gender and author position are correlated.  Definitely worth a read.

An important read: Emma Pierson on gender and authorship position in science

This is a fascinating read: In Science, It Matters That Women Come Last | FiveThirtyEight.  By Emma Pierson, who works at 23 and me.  It has all sorts of references of use and details on authorship position in scientific publications and how gender and author position are correlated.  Definitely worth a read.

Who are the contaminants in your sequencing project? (crosspost from #microBEnet)

This was originally posted on microBEnet: Who are the contaminants in your sequencing project?

Well, been having many discussions recently about PCR amplification happening from "negative" controls where no sample DNA was added. Such amplification is alas pretty common - due to contamination occurring in some other material added to the PCR reaction.  Obviously it would be best to eliminate all DNA contamination of all reagents and all PCRs.  But if that does not happen, it is possible to try to detect contamination after it has happened.  Below I post some papers related to post-sequencing detection of contamination:
Any other suggestions or comments would be welcome. UPDATE 10:30 AM 7/25 - Was reminded on Twitter of a new, critically relevant publication on this issue: Reagent contamination can critically impact sequence-based microbiome analyses