Friday, October 31, 2014

The flawed and offensive logic of "Academic Science Isn’t Sexist" in the @nytimes

OK.  It is Halloween night and I am tired and need to get my kids to sleep.  But someone on Twitter just pointed me to an opinion piece just out in the New York Times: Academic Science Isn’t Sexist - and after reading it I felt I had to write a quick post.

The opinion piece is by Wendy M. Williams and Stephen J. Ceci and discusses work by them (and coauthors).  In particular they discuss findings in a massive report "Women in Academic Science: A Changing Landscape" by Stephen J. Ceci, Donna K. Ginther, Shulamit Kahn, and Wendy M. Williams in Psychological Science in the Public Interest.  I note - kudos to the authors for making this available freely and under what may be an open license and also apparently for making much of their data available behind their analyses.

The opinion piece and the associated article have a ton of things to discuss and ponder and analyze for anyone interested in the general issue of women in academic science.  I am not in any position at this time to comment on any of the specific claims made by the authors on this topic.  But certainly I have a ton of reading to do and am looking forward to it.

However, I do want to write about one thing - really just one single thing -  that really bothers me about their New York Times article.  I do not know if this was intentional on their part, but regardless I think there is a major flaw in their piece.

First, to set the stage -- their article starts off with the following sentences:
Academic science has a gender problem: specifically, the almost daily reports about hostile workplaces, low pay, delayed promotion and even physical aggression against women.  Particularly in math-intensive fields like the physical sciences, computer science and engineering, women make up only 25 to 30 percent of junior faculty, and 7 to 15 percent of senior faculty, leading many to claim that the inhospitable work environment is to blame.
This then sets the stage for the authors to discuss their analyses which leads them to conclude that in recent times, there are not biases against women in hiring, publishing, tenure, and other areas.  Again, I am not in any position to examine or dispute their claims about these analyses - to either support them or refute them.

But the piece makes what to me appears to be a dangerous and unsupported connection.  They lump together what one could call "career progression" topics (such as pay, promotion, publishing, citation, etc) with workplace topics (hostility and physical aggression against women).  And yet, they only present or discuss data on the career progression issues.  Yet once they claim to find that career progression for women in math heavy fields seems to be going well recently, they imply that the other workplace issues must not be a problem.  This is seen in statements like "While no career is without setbacks and challenges" and "As we found, when the evidence of mistreatment goes beyond the anecdotal" and "leading many to claim that the inhospitable work environment is to blame."

Whether one agrees with any or all of their analyses (which again, I am not addressing here) I see no justification for their inclusion of any mention of hostile workplaces and physical agression against women.  So - does this mean that a woman who does well in her career cannot experience physical aggression of any kind?  Also - I note - I am unclear I guess in some of their terminology usage - is their use of the term "physical aggression" here meant to discount reports of sexual violence?   This reminds me of the "Why I stayed" stories of domestic violence.  Just because a women's career is doing OK does not mean that she did not experience workplace hostility or physical or sexual violence.  I hope - I truly hope - that the authors did not intend to imply this.  But whether they did or not, their logic appears to be both flawed and offensive.

UPDATE 1. November 1, 8:30 AM

Building a Storify about this.

UPDATE 2: Nov 3, 2014. Some other posts also criticizing the NY Times piece
UPDATE 3: Nov. 4, 2014.  More posts about the NY Times piece

Thursday, October 30, 2014

Rediscovering some critical terms of use in microbial discussions: #microbiomania and #microbophobia

Earlier this week I was trying to come up with a short term to use when referring to the "Overselling of the Microbiome" and related hype. And I came up with one I really really like: microbiomania. The term just captures the essence of hype about microbiomes to me I guess.

So - of course - the first thing to do was to see if anyone else used this term.  And the number one thing I looked at was domain names.  Nope.  Microbiomania.Com and Microbiomania.Org are now mine.  And then I started to search the interwebs. And surprsingly there was not much (in English at least).  But some links showed up to books in Google Books with passages from > 100 years ago.  And this is when the digging got to be fun.  Here are some of the things I found.

1. A section from "The Medical Era"

When copying this section of the search results I discovered Google Books has an embed tool for Google Books though not sure how well it works: here is a try

Anyway - the text of this section of the book reads:

The Paris correspondent of the Chicago Tribune in a recent letter says We hear very little now of microbist or anti microbist theories Dr Koch's so called discovery is regarded with skepticism though not refuted The truth is his assertions are generally held to be not proven Dr Peters the favorite pupil of the great surgeon Dr Trousseau denounces what he calls microbiomania as a social danger and declares that the micro bians doctrine is vain sterile and objectionable in every way as both needlessly alarming and wrongly reassuring 
So I guess there were some folks who did not like the Koch and his silly theories about germs.

2. The Eclectic Medical Journal Volume 48

Wednesday, October 29, 2014

CEO of Soylent goes even further off the deep end - going after his microbiome

Well, this is pretty deranged: Soylent CEO Is Lifehacking Water By Pissing In the Sink.  Forget all the wackiness of Soylent and the idea of limiting water intake.  And just look at the part of this on the micro biome
Feces are almost entirely deceased gut bacteria and water. I massacred my gut bacteria the day before by consuming a DIY Soylent version with no fiber and taking 500mg of Rifaximin, an antibiotic with poor bioavailability, meaning it stays in your gut and kills bacteria. Soylent's microbiome consultant advised that this is a terrible idea so I do not recommend it. However, it worked. Throughout the challenge I did not defecate.
So - he took Rifaximin to kill his gut microbiome because he thought that would help him not defecate.  And then because he did not defecate he concluded that the Rifaximin played some role in such anti-defecation?  OMFG.  This is both bad science and some, well, crazy a*s-sh*t.  I - I - I - I just do not know what else to say.

Hat tip to Andrea Kuszewski.

Monday, October 27, 2014

Some suggestions for having diverse speakers at meetings

Been having a lot of discussions online in response to my post (Apparently, the National Academy of Sciences thinks only one sex is qualified to talk about alternatives to sex #YAMMM) tracking the awful gender ratio for speakers and session chairs at meetings run by the National Academy of Sciences in their Sackler series.  Some people were asking what one can do to improve gender diversity at meetings so I thought I would post this which I was meaning to do anyway ...


I wrote this in an email to a meeting organizer after I had turned down their invitation due to the imbalance in gender of the speakers (more about this another time --- this is not the same case as the one I wrote about here: Turning down an endowed lectureship because their gender ratio is too skewed towards males #WomenInSTEM). 

Anyway, my colleague wrote a long and very helpful email to me after I withdrew from the meeting when I saw the speaker list.  In the email she detailed things that her organization was trying to do to increase diversity of speakers at meetings.  She ended it with this:
Thus, I take your comment to heart and wanted you to know that I care about this issues as well.  I would love to hear how you balance these inequities at your meetings and learn as much as I can.  Thank you for taking the time to bring this up I know how busy you are and appreciate your candor. Truly looking forward to more scientific exchanges and perhaps some education around gender issues.
And I wrote back, quickly, without digging into the literature or all the posts in the world about this some quick suggestions which I think others might find useful. So here is my response - again - was not meant to cover all the things one can do - just examples:

Thanks so much for the response and I am really glad to see all you are trying to do in this area. 
In terms of how we try to balance inequities at meetings I organize I would note a few simple things
  1. Do not try to invite only the famous people or the people doing the "top" work.  This usually biases one towards more established researchers (as in, older) and this alas also usually is accompanied by distortion of diversity.
  2. DO try to invite people across the breadth of career stages.  Meetings to me should not be only about getting the PIs whose labs are doing the best work to talk.  It should also be about giving opportunities to junior researchers - PhD students, post docs and junior faculty who are doing exciting work - perhaps more focused or smaller scale - but nevertheless exciting.  If one opens up a invited speaker list to people at diverse career stages one generally greatly increases the gender and ethnic diversity. 
  3. DO try to invite people from diverse institutions - research universities, research institutes, companies, non profits, NGOs, the press, non research universities, and more.
  4. DO try to be flexible about times and dates for talks - I have found that women more than men have other commitments (e.g. kids) for which they cannot change dates of activities. 
  5. DO try to provide child care assistance (as you are doing).
  6. DO try to make sure women are on the organizing committee See
  7. DO make sure to provide travel funds.
  8. DO try to include some talks on related areas that may not be the main theme of the conference.  For example history of science and ELSI related topics increase the pool of women and speakers with diverse backgrounds which can be invited.
  9. DO ask the women who turn down invitations if they care to say why.
  10. DO commit to spending a decent amount of time searching for qualified female speakers.  Sometimes there are people who fit ALL the goals of a meeting and they are just missed because women on average have lower public profiles than men doing the same type of work.
Just some ideas off the top of my head.
see also 

Friday, October 24, 2014

Apparently, the National Academy of Sciences thinks only one sex is qualified to talk about alternatives to sex #YAMMM

Just got this email from Francisco Ayala:
January 9-10, 2015 
In the Light of Evolution IX. Clonal Reproduction: Alternatives to Sex 
Organizers: Michel Tibayrenc, John C. Avise and Francisco J. Ayala 
Beckman Center of the National Academies, Irvine, CA 
Evolutionary studies of clonal organisms have advanced considerably in recent years, but are still fledgling. Although recent textbooks on evolution and genetics might give the impression that nonsexual reproduction is an anomaly in the living world, clonality is the rule rather than the exception in many viruses, bacteria, and parasites that undergo preponderant asexual evolution in nature. Clonality is thus of crucial importance in basic biology as well as in studies dealing with transmissible diseases. 
This Colloquium will bring together specialists in various disciplines, including genetics, evolution, statistics, bioinformatics, and medicine. A balance will be sought between the various disciplines, including clonal animals and plants, animal and human cloning, pathogens, and cancer studies.   
Registration is now open
Registration fee is $150. 
Graduate students and postdoctoral researchers are eligible for discount fee of $100. 
All meals, break and reception refreshments listed on the agenda are included in the registration fee.
For more information, contact
Could be interesting right?  Alas, then, I clicked on the link.  And I discovered the meeting could also be referred to as "Only one sex talks about alternatives to sex".  Men are highlighted in yellow. Women highlighted in green. (Note - I am making some guesses as to gender but I think these are reasoably accurate).

Thursday, October 23, 2014

Microbiology Book for Kids: It's Catching by Jennifer Gardy and Josh Holinaty

A few days ago I wrote about how I wanted to share some information about what I have found to be good childrens' science books (based on reading books to my kids).  Well, here is another one: It's Catching: The Infectious World of Germs and Microbes by Jennifer Gardy and Josh Holinaty.

I first became aware of Jennifer Gardy's talents in making catchy microbe-themed kids material when she released the Youtube video "The A-Z of Epidemiology: germs from Anthrax to Zoonoses. A disturbing bedtime book for kids." which is simply awesome. (Note - great animation by Tom Scott):


I watched this video many many many times with my kids - always resulting in painful laughter and entertainment.

I should note that I am collaborating with Jennifer on at least one project (The Kitten Microbiome) and think she is a brilliant scientist and science communicator.  But once I saw her "It's Catching" I realized she really could have a full career as a children's science book and video maker.  It's Catching is both entertaining (like the video) but also educational with information on the history of microbiology and how microbes are studied.  Definitely a good one if you are looking for fun and funny science and/or microbiology themed books for kids.


Wednesday, October 22, 2014

Microbe-themed art of the month: Seung-Hwan Oh portraits w/ mold

OK this is pretty cool (from a microbe-art-science point of view): An Artist Who Paints Portraits With Mold | WIRED.  Seung-Hwan Oh "had to set up a micro-fungus farm in his studio" and he puts film in a warm wet environment (note to self - there could be a new human microbiome aspect of this project depending on what warm wet environment is chosen) and sometimes seeds the system with some mold.  And then he lets nature do its work.

See more about his Impermanence works here. (Really - check out the works - they are wild).

At that site the work is described in the following way:
The visual result of the symbiosis between film matter and organic matter is the conceptual origin of this body of work. The process involves the cultivation of emulsion consuming microbes on a visual environment created through portraits and a physical environment composed of developed film immersed in water. As the microbes consume light-sensitive chemical over the course of months or years, the silver halides destabilize, obfuscating the legibility of foreground, background, and scale. This creates an aesthetic of entangled creation and destruction that inevitably is ephemeral, and results in complete disintegration of the film so that it can only be delicately digitized before it is consumed.
Also see his Tumbl page where one can find many other images like this one:

Hat tip to Kate Scow for posting about this on Facebook.

Sunday, October 19, 2014

Kids' Microbiology Book Review: Germ Stories

I was going through some kids' books today and found quite a few that I thought were wonderful and thought - well - I should post about some of them.  So that is what I am going to do.

The first I want to write about is Germ Stories by Arthur Kornberg with Illustrations by Adam Alaniz and Photos by Roberto Kolter.


I used to read it to my daughter all the time (she is two years older than my son) and then sometimes, when she was older, she would read it to my son.  A few things I like about this book:
  1. It is not all about pathogens - there are sections on yeast, penicillin, gut microbes and Myxococcus (although it is miswritten as Myxobacterium). 
  2. Everything is done as poetry / songs.  Some are cheesy, but my kids liked them.
  3. Each section on a different microbes has a little poem/song, a drawing, and a picture or two as well as a few mini facts (or I guess, micro facts). 
  4. The material is a bit scary / gross at times but not too over the top.
Anyway - I definitely recommend it if you want a microbiology book that will be good for reading to and reading by kids.

I added this book to a collection I am making via Amazon on "Microbiology Books for Kids".  I will write about some of the other ones at another time.

UPDATE - Wanted other suggestions for good kids' microbiology themed books ...

Wednesday, October 15, 2014

Harvard, hope and hype: the sad reason behind overselling diabetes stem cell work - raising money

Earlier in the week I got all fired up - not in a good way - about a press release and news stories relating to a new paper from Doug Melton on a insulin producing STEM cell study
With a little more discussion I just got more angry

I was angry both about the overselling of the implications of the paper and the fact that the paper was not published in an open manner. This was despite the stated goals of HHMI which funds some of the Melton Lab work.

Monday, October 13, 2014

Talk for UC Davis Pre-Health Meeting (#UCDPHSA): Opening up to Diversity

Sunday I gave a talk at the "12th National UC Davis Pre-Health Student Alliance Pre-Medical and Pre-Health Professions Conference".  I normally try to not give talks on weekends (to spend time with my family) but I made an exception here since this meeting has a strong commitment to issues relating to diversity in health and STEM fields.  This mission statement for the meeting reads:
The UC Davis Pre-Health Student Alliance’s objective is to introduce and support academic, admission, and preparatory opportunities for all students interested in health professions with a focus on those underrepresented in healthcare (with regard to gender, economic, social, educational, linguistic, cultural, racial, and ethnic background). We target universities, community colleges and high schools throughout the United States. The UC Davis Pre-Health Student Alliance aims to impact health education, increase diversity amongst the healthcare workforce, and inspire future leaders of healthcare through hosting the largest national pre-health professions conference.
It was that mission statement that got me to ditch my wife and kids Sunday AM (and also much of Saturday PM for a dinner and to work on my talk).  I went to a dinner Saturday for some of the speakers with the new Dean of the UC Davis School of Medicine Julie Freischlag.  The dinner had about 20 or so people and I met some quite interesting folks there working on various aspects of human and animal health.

And then Sunday AM I got up early, decided to use slides (was not sure) and finished off the slide set I had worked on the night before.  I decided that, in the spirit of the meeting, I would talk about two main things - diversity and access.  And I planned to tell three stories about my work in this area.  I wove in some personal stories since, at the dinner the night before Barbara Ross-Lee (who I sat next to) helped remind me of the importance of making talks personal.  So in the end I talked about myself, diabetes, diversity of microbes, antibiotics, diversity in STEM, and open science.  I came up with a title I was OK with: Opening up to Diversity.

My talk went well, I think.  I am pretty sure it was vbideotaped but not sure where that recording will end up. I did however post my slides to slideshare.  See below:

Opening up to Diversity talk by @phylogenomics at #UCDPHSA from Jonathan Eisen

And I also recorded the talk using Camtasia (basically, it allows recording of the screen, the video camera on my computer, and the audio).  I posted the recording (without the video feed which shows mostly my neck) to Youtube.  See below:

Sunday, October 05, 2014

All Nobel Prizes in 2014 Will be Microbially Themed: The Microbes Guarantee It

So - last year I secretly created a microbiome based spying system that can transmit the thoughts and emails of people who they colonize.  I introduced this community into all the people on the various Nobel Prize committees in order to get information in advance about their plans for the Nobel Prizes. After getting such information, and discovering that the Nobel's this year were NOT focused on microbes, I then created a microbiome-behavioral manipulation system and re-infected the Nobel committees with this community.  This community forces their host to think about microbes all the time.  All microbes.  All the time.  And thus I am nearly 100% certain that all the Nobel's this year will be about microbes in some way.

Given that, here are my predictions for the All-Microbial Nobel Prizes.

The Human Microbiome and Methods for Studying Microbial Communities.  Should go to Norm Pace and some other people.  Possibly Jeff Gordon.  Possibly Jo Handelsman.  Possibly others.  Depends on how much the microbes in the committees emphasize themselves versus all microbes.

Vera Rubin for her work on "Dark Matter" since we all know that the key dark matter in the universe is "microbial dark matter".

Discovery and characterizing of the mechanisms of CRISPRs.  No clue who will get this but it likely could include Jennifer Doudna and Emmanuelle Charpentier and others.

Bill and Melinda Gates and their foundation for their work on global health, especially on protecting from infectious diseases.

Literature: Ursula K. Le Guin in particular for her Wrinkle in Time series and its emphasis is on mitochondria.

Well, since microcredit has already won an Economics prize, I am not sure how this will play out but certainly it will involve some type of microeconomics.  Definitely NOT macroecnomics. I think the most likely winner here is Esther Duflo because of her work on both microeconomic topics and microcredit.

Friday, October 03, 2014

Me: Will survey results be published openly. Them: yes. Me: OK - will do survey. #opensurveys

Got this email:
Dear Jonathan, 
Your peers at the University of California, Riverside, Stanford University, and the Coachella Valley Association of Governments are seeking participation in a survey designed to explore the relevancy and perceptions of basic natural history knowledge and skills among professionals and graduate students in environmental science-related fields.
Professionals and Faculty (including post-doctoral researchers) may access the survey through the following link: 
If you cannot complete the entire survey all at once, you can return to the survey within 30 days to complete it at your convenience. 
This survey will be distributed at universities, organizations and agencies state-wide, and we would greatly appreciate your participation! All responses will be kept completely confidential. The information collected will be used to provide summary statistics and form the basis of a peer-reviewed publication. 
Please feel free to forward this survey link to peers within California that may be interested in participating. Thank you for your assistance! 
Should you have questions about this study please contact us:
Michelle Murphy-Mariscal, M.S. (Center for Conservation Biology, UC Riverside)Cameron W. Barrows, Ph.D. (Center for Conservation Biology, UC Riverside)Rebecca Hernandez, Ph.D. (Stanford University, Carnegie Institution for Science)Kathleen Fleming, M.S. (Coachella Valley Association of Governments)
I wrote back
Thanks for the invite.

Can you tell me more about what will happen to the results from the survey? I only participate in surveys if the data and publications from the survey will be released in an open access manner.
Jonathan Eisen

And then got a very pleasing response:
Hi Jonathan, 
Yes, the results and data of the survey will definitely be published. Attached is a previous, survey-based study and we published the data set in Dryad (an online data repository that you are probably familiar with). The survey that my group and I are doing currently will follow the same format and strict adherence to open access. 
Thank you very much for your participation. 
And then I did the survey and sent this email:. 
Thanks so much for the response and I so pleased with your commitment to openness. I will now gladly participate and share w/ California colleagues.

Why I Tweet and Blog: Captured by Beryl Lieff Benderly

You know, many people ask me - why do I talk to science reporters so often.  They ask this and then claim that science reporters are just all kinds of evil because they always get quotes and facts and concepts wrong.  Well, that has really not been my experience.  Sure, I have my examples of problems.  But overall, I have been impressed and pleased more often than not.  And here is a great example. I was interviewed a while back by Beryl Lieff Benderly about my somewhat obsessive experimentation with social media for communicating science.  And then, of course, I forgot about it.  So I was exceptionally pleased when I saw the story come out today: To tweet or not to tweet? | Science Careers.  Beryl did a remarkably good job in capturing the essence of my thoughts about Tweeting, Blogging, social media, and science communication.

If you want to know what I think about how to not get overwhelmed with Twitter, how to not spend too much time on social media, and what I think abotu aboutb social media, you don't need to wait for me to try to write my thoughts on the topic down.  Read what Beryl wrote.

Wednesday, October 01, 2014

Crosspost from microBEnet: Some interesting new papers on functional analysius of metagenomics

Crossposting from microBEnet:

Some new papers that may be of interest to people:

Crosspost from microBEnet: Collection of papers on "The Science of Science Communication"

Crossposting this from microBEnet 

 Just got pointed to this by Sharon Strauss, the chair of the Evolution and Ecology department here at UC Davis: The Science of Science Communication II Sackler Colloquium.  This is a collection of papers from a colloquium held in Septment 2013.  Slides and videos of the talks are available online. The papers and links (copied from the PNAS site) are listed below.  There are many papers here of relevance to work done at microBEnet and are also likely of general interest to many: