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. 
Sincerely, 
XXXX
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:

XXX 
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. 
Sincerely, 
Jonathan Eisen
For related posts by me see my collection on Diversity in STEM.

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?  


Jesica Mack has left a new comment on your post "Science SPAMMER of the month: OMICS publishing gro...":

For me it has been a surge of meeting welcomes, for the most part in China, having nothing to do with my examination: bentham science publishers.
-----
Jesica Mack has left a new comment on your post "I am highly skeptical of the CHORUS system propose...":

I don't see anything in this that seems particularly useful.Please click: bentham science publishers
-------
Jesica Mack has left a new comment on your post "Wow - Google Scholar "Updates" a big step forward ...":

Snap. I likewise found this advancement a couple of days prior and discovered one recommended paper of immediate pertinence.Please click:bentham science publishers

------
Jesica Mack has left a new comment on your post "ADVANCE Journal Club: Developing Graduate Students...":

This is very interesting I appreciate this effort.Please click:bentham science publishers

-----
Jesica Mack has left a new comment on your post "UCDavis IT and GMail think this "Open Journal of G...":

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



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 ...

Fun times with whooping cough in #DavisCA

Just got this email.  I have removed the specific sender / facility since that does not seem needed for my purposes here.  I have replaced the name of the site with "Our Facility". Anyway - thought some people would be interested in the things that can happen when too many people in your community do not vaccinate their kids.

From: Office Administration 
Subject: Possible Exposure to Whooping Cough - Pertussis
Date: June 25, 2014 at 12:55:59 PM PDT
To: Office Administration 

Dear Parent or Guardian,

Our Facility was informed this morning that a student who has been attending a class since 6/16/14 has been diagnosed with pertussis (whooping cough). The child is no longer attending the class and is under a medical care.

If you feel you or your child may have been exposed, watch carefully for symptoms in the next 1-2 weeks, and consult a physician if any occur. Here is some pertinent information regarding pertussis (whooping cough):

Pertussis can spread through the air when people cough. It often starts like a common cold which gets worse and worse over 1-2 weeks. People with pertussis have coughing spells that may last several seconds. As they catch their breath at the end of each coughing spell, they may gasp loudly (“whoop”) and vomit or choke.

The vaccine usually protects against pertussis, but sometimes even immunized children can get pertussis. Pertussis is treated with antibiotics. Antibiotics can also prevent the spread of pertussis to others.

Activities that may help stop the spread of pertussis include:
  • The exclusion of all pertussis cases from classes until they have taken the first five days of the antibiotic.
  • The administration of antibiotics for babies, pregnant women and other high risk contacts of pertussis cases as well as consideration of antibiotic administration for other household or close contacts to prevent the further spread of pertussis.
  • The administration of another dose of DTaP vaccine to babies and Tdap for older children who are not up to date on their vaccine series.
Please know that Our Facility is taking every precaution in this matter and let us know if you have any questions or concerns.

Sincerely,

Office Staff

Please make it stop - overselling the microbiome award for rugby, exercise, microbiome stories

Well, I think today's lesson is, many people, including many scientists and science reporters, just do not get that there is a difference between correlation and causation.  I know - this is like beating a dead horse since many write about this issue.  But it just needs to be called out every time until it stops.  And today's fun comes from stories and the original research articles about how exercise supposedly alters the gut microbiome.

I was pointed to this just a few minutes ago on Twitter:


In this Tweet Bernat Olle points to a "news" story in Medpage Today: Exercise Boosts Gut Microbiome Diversity by Kristina Fiore.   Well, so of course I started digging around.  And, not surprisingly, the study that this is based on shows absolutely no causal connection between exercise and the gut microbiome.  The study is in the journal "Gut": Exercise and associated dietary extremes impact on gut microbial diversity.  And here is what they did:
  • They selected subjects - 40 "elite" rugby players.
  • They identified healthy male "controls" with similar age and size and from similar place. 
  • Then they collected faecal and blood samples from participants and did surveys about their nutrition and clinical data.
  • Among many measurements, they did 16S sequencing from the fecal samples
  • Then they did some bioinformatics and found differences between the rugby players and the controls in many features including microbiomes.
And amazingly, from this they report, in their abstract
The results provide evidence for a beneficial impact of exercise on gut microbiota diversity but also indicate that the relationship is complex and is related to accompanying dietary extremes.

Discussion of new pathogen discovery papers

Interesting discussion yesterday with authors of new pathogen discovery papers. I will try to write more about this later but am heading out the door so this Storify will have to do for now.

ASUCD (Associated Students, #UCDavis) Excellence in Education Awards

Very proud of this.  I was a finalist in the "Excellence in Education" awards given out by the UC Davis Undergraduate group ASUCD Associated Students, University of California, Davis. And David Coil, Project Scientist in my lba was another finalist. The award for my college (College of Biological Sciences) went to Jay Rosenheim, who is a great teacher, so no shame in losing to him.




 Anyway - here are some pics.

One of the ASUCD members doing introductions
Another ASUCD
David Coil getting is certificate
Hey, that's me
Jay Rosenheim getting his certificate

Love this - The Aggie Transcript #UCDavis Undergraduate Life Sciences Journal

I just love things like this: The Aggie Transcript | An undergraduate life sciences journal at UC Davis.  From their site:

The Aggie Transcript is is a forum for undergraduate UC Davis students to share news, original writing, and art related to the life sciences.
Here are some recent posts:



What a great idea.


CAMERA metagenomics resource is shutting down

Just got this email and thought it would be of interest to many out there.

Thank you for being a CAMERA user during its operation as a resource for
environmental genomics. During the past few years, CAMERA has been able to
offer a number of important community resources, including an exceptionally
well curated environmental genomic database, the ability for researchers to
deposit molecular sequence datasets with associated environmental
parameters (metadata), open access to computational resources to enable
metagenomic comparisons, educational resources, and helpdesk services.
These efforts have been funded through the Gordon and Betty Moore
Foundation (GBMF) Marine Microbiology Initiative and the National Science
Foundation to serve the needs of the marine microbiology community and
other users.
In particular, the CAMERA compute resources, which include large-scale
BLAST capabilities and other workflow-enabled analysis capabilities
(RAMMCAP), were generously supported by the GBMF, the San Diego
Supercomputer Center, the NSF XSEDE program, and commercial Cloud computing
resource providers (CODONiS).
Due to the termination of GBMF support, CAMERA can no longer accommodate
the computational needs of the community. Therefore, starting July 1, 2014,
CAMERA will begin to shut down the CAMERA portal and will no longer accept
any new workflow submissions. The results of workflows submitted by July 1,
2014 will be available to users through July 15th. Urgent requests for the
temporary use of CAMERA workflow resources beyond July 1, 2014 will be
considered on a case-by-case basis.
If you are a current or prior CAMERA user and would like to retrieve
personal data from the system, we strongly encourage you to do so now.
As announced earlier this year, CAMERA will continue to maintain free and
open access to its rich collection of curated data and metadata via the
CAMERA Data Distribution Center (DDC), which includes links to the Marine
Microbial Eukaryote Transcriptome Sequencing Project. In conjunction with
the portal shutdown, CAMERA will also no longer accept user data
submissions past July 1st (but data submissions currently in progress will
be completed and made available via the DDC).
Please contact us at camera-info@calit2.net regarding matters pertaining to
the use of CAMERA.
Thank you so much for your support and participation!

Gulp - a good book for those into, well, our insides

On Saturday I went into downtown Davis, CA with my kids to get them haircuts and then to get a present for one of their friends for a birthday party. We decided to get a present at Avid Reader downtown. And after looking for the gift and for some books for my kids I decided I wanted to check out their science section. And I came up with a present for myself too


And then started reading it. It is quite good.

On top of reading the book I have been checking out some interviews with the author Mary Roach. Quite entertaining. For example I was pointed to one on Twitter:


And I then remembered I had been pointed to another via email a while back by Steve Faith at UC Davis:  A Brief Tour Of The Alimentary Canal, From Spit To You Know What : Shots - Health News : NPR.
Still not done with the book but if you want a great read about our insides - I recommend Gulp by Mary Roach very highly.