Saturday, July 26, 2014

Bat tour at Yolo Basin Wetlands

Did our second evening bat tour at the local Yolo Basin Wetlands last night.  It was very nice.  They start off with a lecture and bat introduction at the Visitor Center and then a convoy heading out to the wetlands and drove way way into the back (the side near Sacramento) to just next to the causeway.  Then we waited until sunset and out came the bats.  Thousands and thousands of them.  It was cool.  Here are some videos and pics.  And also some responses to my Tweets about it.

Thursday, July 24, 2014

How do journals like this even exist? Lovely spam! Wonderful spam!

Just got this email.  I consider this almost unquestionable proof that this is a spam open access journal (e.g., I don't do any work in this field ..)

Dear Dr. Jonathan A. Eisen,

Greetings from the Journal of Immunology and Immunotherapeutics!!!

At the outset, it’s your eminence & reputation in the quality of research field for which you have been invited to become Editorial Board member for our Journal.  We are aware of your reputation for quality of research and trustworthiness in the field of “Immunology and Immunotherapeutics” and that is why you are being requested to be an Editorial Board Member of our journal entitled “Journal of Immunology and Immunotherapeutics”.

 Please go through the URL for Journal home page:

IMPRINTS Online Publishing uses online review and editorial tracking systems of Editorial Manager® / IMPRINTS Group for quality review process. All works published by IMPRINTS Publishing Group are under the terms of the Creative Commons Attribution License. This permits anyone to copy, distribute, transmit and adapt the work provided the original work and source is appropriately cited. IMPRINTS Publishing Group supports the Bethesda statement on Open Access publishing.

We may again assure you of international quality and standards of our articles published in our journals, using state-of-the-art prominent reviewers and editorial board. We also assure you of our best co-operation always.

If you are interested, you are requested to send a recent passport size photo (to display at our website) and your C.V, Biography (150 words), Research Interests for our records.

We look forward to a close and lasting scientific relationship for the benefit of scientific community.

With best regards,

Stephen H
Managing Editor

Immunology and Immunotherapeutics

Monday, July 21, 2014

Turning down an endowed lectureship because their gender ratio is too skewed towards males #WomenInSTEM

Just got this invitation.  I have edited it to remove some of the identifying factors since I think the specific details do not matter.
Dear Dr. Eisen: 
I am writing to invite you to present a lecture in the endowed XXXX Lecture Series at XXXX Univsersity.  The XXXX Lecture is a platform to allow leaders in the areas of XXXX to communicate research advances to a general audience.  Recent speakers include XXXX and XXXX and XXXX.  For your talk, we were hoping you could discuss advances in understanding human microbiomes and their significance to health.  I think this is an enormously important area that the general public is still largely unaware of, and also an area with incredible promise that will see exponential progress going forward.  I know this is relatively short notice, but we are hoping that the lecture would be sometime in October or November of 2014. 
The lectureship includes an honorarium of $2,000 in addition to covering your travel, lodging, and meal expenses.  Because XXXX we generally hold duplicate lectures XXXX on consecutive evenings (typical Tues-Wed or Wed-Thurs).  Speakers generally arrive early in the afternoon of the day of the first lecture, and depart after the second lecture the following day. Between the two lectures there will be a dinner and meetings with research or medical groups and an outreach activity in which, if you are willing, you would XXXX. 
We would be honored to have you speak in the XXXX series  and hope you will be able to fit us into your busy schedule. 
Well, wow.  That would be really nice.  I do not think I have ever given a named lecture before.  Then I made one fateful decision - I decided to look up who had spoken at the lecture series previously.  And, well, it was not what I wanted to see.  And another lecture series from the same institute had the same problem.  Bad gender ratio of speakers.  So, after some thought and a brief discussion with a post doc in my lab Sarah Hird whose opinions I trust on such issues.  I wrote this to the people who invited me:
Thank you so much for the invitation and the respect it shows to me that I would be considered for this.  However, when I looked into past lectures in this series I saw something that was disappointing.  From the site XXXX where past lectures are listed I see that the ratio of male to female speakers is 14:3.  I note - the XXXX lecture series - also from XXXX - also has a skewed ratio (11:2).  As someone who is working actively on multiple issues relating to gender bias in science, I find this very disappointing.  I realize there are many issues that contribute to who comes to give a talk in a meeting or seminar series or such. But I simply cannot personally contribute to a series which has such an imbalance and I would suggest that you consider whether anything in your process is biased in some way. 
Jonathan Eisen

UPDATE 7/22/2014

The person who invited me responded to my email.  Here is what this person wrote:
Thanks for response and your concern.  I noted this uneven representation also when I took over the series a couple years ago and have worked (not as successfully as I would have liked) to get more balance.  For example, in trying to book the XXXX lecture this year I have been turned down by XXXX, but did manage to book XXXX.  For the XXXX lecture series, a related but separate series aimed at professional rather than the lay public audiences that I also run, I was turned down by XXXX, but I’ve booked XXXX.  You have been the sole male invite to either series this year.   But I will agree that in previous years the ratio has not been as good as I would like.  In part this is because it seems even harder to book top female speakers than males speakers - presumably because they are in such demand and are always asked to be representative on a million committees etc, but in past XXXX I did bring in XXXX and XXXX.  For the XXXX lecture I brought in XXXX last year.  So numbers are getting better, and this year the ratio will be at least 2:1 (max) in favor of females. 
But you point is well taken, and perhaps I can even things out a little with your help.  Although I think microbiomes are an incredibly important and under appreciated area, this is not my area of research, so I don’t know the players.  If you can recommend female researchers in this area who are dynamic speakers that would be able to give a very publicly accessible talks (TED talk level) on the topic, and ideally are also doing great research too, I would be happy to invite them.  
So then I wrote back
Ruth Ley at Cornell is great - works on evolution of microbiomes and
has done some fantastic stuff in humans and plants. See And gives very good talks. 
Katie Pollard at UCSF is completely brilliant and awesome and gives
amazing talks She works on many things including microbiomes 
Jessica Green at Oregon does not work
on human microbimes per se but does work on microbiomes in buildings
and connects that to human microbiomes.  She is also a TED fellow and
has given two great TED talks and is one of the best speakers I know. 
Julie Segre at NHGRI is great too.  Hard core medical microbiome work:

UPDATE 2: Storify of responses

UPDATE 3: Some links writing about this

For related posts by me see my collection on Diversity in STEM.  Some key posts of possible interest include:
Other diversity related posts

Saturday, July 12, 2014

Is this a new form of #OpenAccess Spam - spammy blog comments pointing to Bentham

Well, this is very very weird and not sure what to make of it.  In the last week the filter that Google runs for Blogger Comments has picked up a slew of highly spammy comments coming from one account.  And all of the comments include a link to Bentham Science publishers - one of the annoying Spammy new publishers. See some of them below (note I have removed the links to Bentham but trust me, this went to a Bentham site).  Anyone else getting Spam comments pointing to Bentham?  

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What's particularly annoying about all these SPAM journals is that they are training filters to ignore legitimate journal activity.Please Click:bentham science publishers

Thursday, July 10, 2014

Paper of interest: Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease

For those interested in microbiomes it is definitely worth looking at this paper: BMC Genomics | Abstract | Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease

Simple summary - they have sets of identical twins where one twin has Crohn's and the other does not.  They looked for somatic mutations that could like the ones with Crohn's and did not find any.  Sure - a negative result.  Could be anything.  But the next obvious thing to do (which they report they are already doing) is to look at the microbioata in these people.  Alas, they probably do not have data from before these people got Crohn's, but still, this could be interesting ...