Saturday, August 30, 2014

A tale of salt and gender: participation of women in halophile research

Interesting paper on women in science of direct relevance to my work: Frontiers | Salty sisters: The women of halophiles | Extreme Microbiology.  I have been working on halophilic archaea for many years (since introduced to them in graduate school) and published papers on this topic (e.g., see The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon and Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux and more coming).  However, I have never been to a meeting dedicated to the topic and confess I have not thought specifically about the gender of scientists in this field and at meetings in the field and such.  Thus I was pleasantly surprised to see this analysis from Bonnie Baxter, Nina Gunde-Cimerman and Ahoren Oren.  Their abstract is below:
A history of halophile research reveals the commitment of scientists to uncovering the secrets of the limits of life, in particular life in high salt concentration and under extreme osmotic pressure. During the last 40 years, halophile scientists have indeed made important contributions to extremophile research, and prior international halophiles congresses have documented both the historical and the current work. During this period of salty discoveries, female scientists, in general, have grown in number worldwide. But those who worked in the field when there were small numbers of women sometimes saw their important contributions overshadowed by their male counterparts. Recent studies suggest that modern female scientists experience gender bias in matters such as conference invitations and even representation among full professors. In the field of halophilic microbiology, what is the impact of gender bias? How has the participation of women changed over time? What do women uniquely contribute to this field? What are factors that impact current female scientists to a greater degree? This essay emphasizes the “her story” (not “history”) of halophile discovery.
As part of their paper they analyze participation of women at conference on halophiles:

This is a useful analysis and compendium and it would be great to see this done for as many fields as possible. 

Mesquite "A modular system for evolutionary analysis" v3.0 released from Team Maddison

Just found out about this on Facebook via Rod Page: Mesquite V3.0  has been released.  Mesquite is from Team Maddison (Wayne and David).  I have been using their software since 1987 when I took Stephen Jay Gould's course at Harvard and they were TAs for the course demoing an early version of MacClade.   Lots of nice features and it is available in Mac, Unix/Linux, and Windows versions.   They describe "What Mesquite Does" on their Wikispaces site in the following way:

Mesquite is software for evolutionary biology, designed to help biologists manage and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses and management features available depend on the modules installed. Here is a brief overview of some of Mesquite's features. See also a more complete outline of features, and the Mesquite Project Youtube channel, with instructional videos helping you learn Mesquite.

Despite Mesquite's broad analytical capabilities, the developers of Mesquite find that we use Mesquite most often to provide a workflow of data editing, management, and processing. We will therefore begin there.
Definitely worth a look.

NIH Announces Revised Genome Data Release Policies

Just got notified of this by the UC Davis Med. School grants administration: NOT-OD-14-124: NIH Genomic Data Sharing Policy.  Lots of interesting things in here including a summary of the comments that they received on the draft policy.

I have copied some of the more interesting and relevant bits below:
  • Sharing research data supports the NIH mission and is essential to facilitate the translation of research results into knowledge, products, and procedures that improve human health.  NIH has longstanding policies to make a broad range of research data, in addition to genomic data, publicly available in a timely manner from the research activities that it funds. 
  • The public comments have been posted on the NIH GDS website.
  • The statement of scope remains intentionally general enough to accommodate the evolving nature of genomic technologies and the broad range of research that generates genomic data.
  • Several comments were submitted by representatives or members of tribal organizations about data access.  Tribal groups expressed concerns about the ability of DACs to represent tribal preferences in the review of requests for tribal data.
  • The GDS Policy expects that basic sequence and certain related data made available through NIH-designated data repositories and all conclusions derived from them will be freely available.  It discourages patenting of “upstream” discoveries, which are considered pre-competitive, while it encourages the patenting of “downstream” applications appropriate for intellectual property.  
  • NIH expects investigators and their institutions to provide basic plans for following this Policy in the “Genomic Data Sharing Plan” located in the Resource Sharing Plan section of funding applications and proposals.  Any resources that may be needed to support a proposed genomic data sharing plan (e.g., preparation of data for submission) should be included in the project's budget. 
  • Large-scale non-human genomic data, including data from microbes, microbiomes, and model organisms, as well as relevant associated data (e.g., phenotype and exposure data), are to be shared in a timely manner. 

Friday, August 29, 2014

Kudos to Dr. Roizen's Personalized, Preventive, & Integrative Medicine "Focus on Women's Health" Conference #NoMoreYAMMMs

Quick post here as I have a bit of a cold.  I post a lot of critiques here about meetings that have bad gender ratios for the speakers.  But I do focus on the negative and am trying to also call attention to the good cases.  Well here is one: the 12th Annual Dr. Roizen’s Personalized, Preventive, and Integrative Medicine Conference with a focus on Women's Health.  And unlike the recent Ovarian Club meeting (see No Ovaries? Well this Ovarian Club Conference is For You (YAMMMs for everyone)) which had few female speakers despite the topic, Dr. Roizen and the other organizers (including one of my favorite colleagues Rosane Oliveira) did a great job.  The gender ratio of organizers, moderators and speakers all looks good (see images below).  Kudos to all involved.

Tuesday, August 26, 2014

Overselling the Microbiome Award: The Microbiome Diet Book

Well, umm, I do not know what to say: The Microbiome Diet: The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss: Raphael Kellman MD: 9780738217659: Books.  I got pointed to this book by Dorothy Timmermans and she wondered if this was a case of "overselling the microbiome" or not.  I guess I don't know because I have not read the book.  Nor will I most likely.  But I think almost certainly it is a case of "Overselling the Microbiome" based just on reading the blurb on Amazon from the Publisher which I paste below.  It contains a litany of over the top statements:

Cutting-edge science has shown that the microbiome is the secret to healthy weight loss and to feeling healthy, energized, optimistic, and at the top of your game. The microbiome is a whole inner world that lives within your intestines—trillions of tiny microbes that help you extract the nutrients from your food, balance your mood, and sharpen your clarity and focus.

These beneficial bacteria make up a separate ecology within the body and have an enormous influence on your metabolism, your hormones, your cravings—even your genes. The microbiome's health is intimately involved with yours: when it flourishes, you flourish. When it craves sugar, so do you. When it operates at peak efficiency, so does your metabolism. And when your microbiome is out of balance, you might find yourself gaining weight or unable to lose weight, no matter how much you exercise or how carefully you eat. To achieve your ideal weight, you need the help of your microbiome.

Now, drawing from nearly two decades of experience as a specialist in functional medicine and intestinal health, Raphael Kellman, MD, has developed the first diet based upon on these scientific breakthroughs. The Microbiome Diet offers an effective three-phase plan to heal your gut, reset your metabolism, and achieve dramatic, sustainable weight loss. The Microbiome Diet will help you...

Reset your metabolism

Free yourself from food cravings and uncontrollable appetite

Incorporate prebiotics, probiotics, and healing foods into every meal

Lose weight—and keep it off—with a nonrestrictive life plan

With delicious recipes, convenient meal plans, and helpful information on Microbiome Superfoods and Supersupplements—including prebiotics and probiotics—The Microbiome Diet gives you the tools to achieve your healthy weight, boost your mood, regain your mental focus, and be in your best shape for life.

Sound too good to be true?  Well, that is because it is.

Monday, August 25, 2014

The Agricultural Bioscience International Conference #ABIC2014 run by @ABICFoundation: where you can hear lots of talks by men #YAMMM

Well, here is this week's YAMMM (yet another mostly male meeting) alert: The Agricultural Bioscience International Conference in Saskatchewan.

Male Speakers: 40
Female speakers 4

  1. Marc Albertsen
  2. Robert Carberry
  3. David Fischhoff
  4. Maurice Moloney
  5. Frédéric Seppey
  6. Juliana Alexandre
  7. Tom Carrato
  8. Michael Frodyma
  9. Carlo Montemagno
  10. Tim Sharbel
  11. Simon Barber
  12. David Chalack
  13. Richard Gray
  14. Giuseppe Natale
  15. Roman Szumski
  16. Roger Beachy
  17. Raju Datla
  18. Wayne Hunter
  19. Matthew O'Mara
  20. Albert Vandenberg
  21. Suzanne Bertrand
  22. Swapan Datta
  23. David Irvin
  24. Peter Phillips
  25. Victor Villalobos
  26. Julie Borlaug
  27. Maurice Delage
  28. Lawrence Kent
  29. Ingo Potrykus
  30. Simon Warner
  31. Jim Brandle
  32. David Dent
  33. Ganesh Kishore
  34. Andrew Potter
  35. Howard Wheater
  36. John Buchanan
  37. Claude Fauquet
  38. Robert Lamb
  39. Thomas Redick
  40. Hong-Wei Xue
  41. Derek Byerlee
  42. Nina Fedoroff
  43. Greg Meredith
  44. Andrew Reed

Who gets the credit/blame for this wonderful arrangment? 
  1. Chair, Wilf Keller, Ag-WestBio Inc.
  2. Jerome Konecsni, Innovation Saskatchewan
  3. Muriel Adams, ABIC Foundation
  4. Art Froehlich, Ad Farm
  5. Pierre Fobert, National Research Council
  6. Graham Scoles, University of Saskatchewan
  7. Peter Phillips, Johnson-Shoyama Graduate School of Public Policy
  8. Paul McCaughey, Agriculture and Agri-Food Canada
  9. Dr.Abdul Jalil, Saskatchewan Ministry of Agriculture (originally colored green)
  10. Janice Tranberg, Saskatchewan Ministry of Agriculture

This goes with another YAMMM from Canada recently: Today's YAMMM (Yet Another Mostly Male Meeting) Brought to You by CIFAR & NAS.  I have not done any analysis of meetings organized by country but I am thinking it might be worth looking into.  I would really suggest if anyone is considering going to this meeting for you to skip it.  There should be consequences for such a skewed ratio.  And while you are at it consider writing to the organizers and sponsors.  I will ...

Friday, August 22, 2014

Want to prevent someone from taking copyright on something- have it be made by a monkey

Well, this is both strange and surreal and fascinating: Who Owns A Monkey's Selfie? No One Can, U.S. Says : The Two-Way : NPR.  Turns out the UC Copyright office says a photo taken by a monkey cannot by copyrighted because apparently copyright is reserved for humans (and I guess human corporations).  NPR implies that an Ars Technica article by David Kravets is what caught their attention as well as that of others.

I wonder - if one could teach a monkey to type maybe one could get them to type up some papers and then nobody could have copyright on them?  What if one wrote a paper where a monkey was a co-author but did not do all the work?  Would that mean one could not transfer copyright to anyone else?  Seems like I should / could include monkeys on all my work.

Thursday, August 21, 2014

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

Wednesday, August 20, 2014

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.


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. 

Monday, August 18, 2014

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.

Friday, August 15, 2014

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 has announced his first action as Publisher - a partnership between AAAS and Snapchat (

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 for details.


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

So I wrote back

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. 
Jonathan Eisen 

Thursday, August 14, 2014

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.

Friday, August 01, 2014

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