Monday, March 19, 2018

Science Magazine publishes "opinion" piece targeting a specific student w/ sexist "critique" and then won't publicly discuss what happened or what they will do about it

Well, I can't even begin to explain how disappointed I am in AAAS and Science Magazine over their actions recently. An "opinion" article was published last week in the "Working Life" section of Science which was stunningly inappropriate for Science Magazine. I first found out about this when I saw a Tweet from a colleague and friend Rebecca Calisi Rodriguez.
And when I started to dig into the story I was nauseated.

 To sum up - the article was by a student who was apparently trying to express some thoughts about #SciComm activities by others that she did not like. And in the piece she named and mocked the activities of another PhD student at her own institution who does SciComm in ways she does not feel comfortable with. Fortunately, when I started looking at social media responses to this, they were overwhelmingly in support of this targeted student - Samantha Yammine who does really quite phenomenal SciComm work. (See for example her Twitter feed and her Instagram feed.

 I am really thrilled and proud of the community that came out in support of her.

There have also been a few news stories related to or directly about the topic which are worth reading.
Also some of the Tweet streams about this are really worth reading. For example, this one from @christineliuart is a must read:

I ended up compiling some of the Tweets about this topic in a Twitter Moment which I share below. 

Hopefully, the student who wrote the article will rethink many aspects of it and hopefully she does not suffer major repercussions from writing this misguided piece.  And though she originally seemed to be defending the article she eventually at least posted an apology to Sam.

 However, there is one part of the story that I believe is in need of a major, detailed examination.  And that is the role of Science Magazine in all of this.  I went on a bit of a rant about this on Twitter when I and other people found that Science's response to the controversy was insufficient.  I embed my posts about that below.

So I started to dig around into what I could do and then I got an email from the Editor in Chief of Science. Apparently, after publishing an article that directly critiqued a PhD student in public in his own magazine he was uncomfortable with responding in social media.  I am not sure whether Jeremey Berg thinks these emails should remain private but I do not think that.  So I am posting my exchange here.

Hi Jonathan: I would like to understand better your views on the Working Life column but I do not think Twitter is the best forum for this. The full Editor’s note is shown below:

Editor's note, 17 March, 12:45 p.m.: In setting the context in this opinion piece, an individual (Science Sam) was identified and many have read the article as a personal attack. This was not the intent of the author or the editors, and we apologize. We are examining our editorial process for these pieces moving forward.

This is an honest assessment of what happened. The author’s concerns about what she perceived as an expectation for her, as a woman, to participate in a certain type of science communication was driven by promotion of this on her campus.

In retrospect, the piece should have been edited so that the person was not identified, but it was not intended to be an attack and was not read this way by several editors and many other readers.

What do you think will be accomplished from “a more thorough investigation”?

I welcome your thoughts.

Best, Jeremy

Jeremy M. Berg, Ph.D.

Editor-in-Chief, Science family of journals
So I wrote back immediately

Thanks for the email. 
A few comments

1. The author said on Twitter she worked extensively with an editor to craft her piece. I think it is important to know if it was ever discussed that she identified a specific person for her critique and whether they considered that to be a good or a bad thing. For that matter, how was this introduced to the piece - did it come from the author or from the editor?

2. Does Science Magazine have any policy of any kind regarding personal attacks / critiques like this? If yes, were they ever considered in this case? If no, why not?

3. During the editing process, was there ever a discussion of how to get more attention to the piece? I can only assume yes so in that context what was discussed? Did the mocking, demeaning wording come from the editor or from the author and why was it not removed?
  • For example consider "Publicly documenting the cute outfit I wear and the sweet smile I brandish." Given that the article publicly identifies the target of this piece, it is reasonable to assume this is targeting Sam. This is just not OK.
  • And furthermore, who chose to highlight that one line in the piece. Yes, it is catchy. But it is a personal attack against a female graduate student. And it is astonishing that it was published.
4. Why was it deemed reasonable for such a piece to repeatedly disparage outreach efforts of others? Is this a useful thing to publish in this space?

Some examples
  • ".. I am annoyed that the majority of the posts seem to celebrate a very narrow representation of femininity,"
  • "demonstrate that they're interested in clothes and makeup, that they're physically active, and that they are attractive romantic partners"
  • " Time spent on Instagram is time away from research"
  • "Let's not celebrate that."
I believe there is no way to interpret this other than an attempt to shame people like Sam. This basically is saying "you cannot do this - you are to be shamed for focusing on such things".

And that is disgraceful.

5. Are you and Science going to publicly apologize to Sam?

6. Why does this piece not suggest alternative uses of Intagram? Why is it just attacking what other people do?

And much more. I think this article, being published in Science, with the editing help of Science, is in need of a thorough investigation to find out why it ended up the way it did. Why was there a personal attack left in? Why was it deemed OK to mock other people? Why could it not instead have focused on positive suggestions for how to do outreach in other ways that maybe Meghan was OK with? And so on.

I encourage you to have a more public, open discussion of how this happened and how you might try to prevent it from happening again.

And eventually I got a response back from Jeremy
Hi Jonathan: Thanks for your response.

The story unfolded as described in the piece. The author was introduced to Science Sam’s Instagram efforts at a career workshop, started looking into this and other Instagram accounts, found herself uncomfortable with the content and her perceived expectation that she follow suit, and did some self-reflection to conclude that she resented the implications regarding the underlying issues related to women in science. Based on this, the author wrote her essay and submitted it to Science Careers. Her experience with Science Sam’s Instagram account was always a central part of the essay. The editing process involved working with her on the writing to help make her message clearer. There was no attempt to get more attention to the piece or to make it more inflammatory.

I think the perspective that some young female scientists feel pressured to participate in science communication efforts, particularly those of a specific type, is an interesting one. I do not read this as an attempt to disparage the efforts of others but rather to explore the basis for the author’s reactions to these efforts.

We have both publicly and privately apologized to Samantha.

As I said in my earlier email, in retrospect, we should have explored ways to avoid naming an individual specifically in the essay, both to avoid the appearance of an attack and the loss of the message of the essay over this issue. As we indicated in the Editor’s note, we are examining our processes related to these pieces.

Best, Jeremy

Jeremy M. Berg, Ph.D.

Editor-in-Chief, Science family of journals
It did not, well, make me feel like Science was going to be doing anything. And many parts of the response I find troubling.  But I could not deal with all of that.  I focused on what they planned to do in terms of looking into what happened and wrote back.
I have many questions and comments and concerns about your response here but want to focus on one issue. 
What do you mean by "we are examining our processes related to these pieces." Can you say more about your plans in this regard? 
And I got back an even more disappointing response
Hi Jonathan: At this point, there is not much more to say. The people involved in the process will meet and discuss whether we need to do anything differently to avoid potential problems in the future.

Best, Jeremy

Jeremy M. Berg, Ph.D.

Editor-in-Chief, Science family of journals
So - basically, it looks like Science Magazine will do nothing. They published an inappropriate article targeting a single PhD student and that article was also loaded with a variety of sexist misguided attacks on specific types of science communication.  And they won't discuss this on Twitter because it is not the right place to discuss it.  And then by email they basically state "We will privately look into it and not tell anyone."

That is just not enough.  I plan to pursue this further via AAAS and see if a formal, perhaps outside review can take place.

YAMMMM: Yet another mostly male microbiome meeting - Microbiome Therapeutics Europe Meeting

YAMMMM: Yet Another Mostly Male Microbiome Meeting:
Microbiome Therapeutics Europe Meeting

From their speakers page I estimated gender balance of speakers 

19:6 M:F 
or 75% male

Thursday, March 15, 2018

YAMMMM - Yet another mostly male microbiome meeting - 2018 Translational Microbiome Conference


Here is a sad sad example of a YAMMMM - yet another mostly male microbiome meeting (a phrase first coined by Carly Rosewarne).

The 2018 Translational Microbiome Meeting.

From my estimates there are 47 speakers of which 41 are male (note - these are inferences of gender and may be inaccurate).  That comes out to an estimate of 87% male speakers.  That is just not good.  The microbiome field has a good sample pool of people of diverse backgrounds that could be speakers at meetings and thus meetings that are this skewed in diversity should not be supported.


Friday, March 09, 2018

Frustrated by YAMMMMs: Yet another mostly male microbiome meeting

UPDATE 3/9/2018 - See Comments.  Carly Rosewarne coined the term last year ...

A while back I coined the term "YAMMM" - yet another mostly male meeting - to reflect my frustration in seeing meetings where most of the presenters were male:

What to do when you realize the meeting you are speaking at is a YAMMM (yet another mostly male meeting)?

I have since written dozens of posts about such meetings.  Sadly this is not an unusual thing.  Fortunately there has been a growing movement in many communities, including in science, to critique and not support such "MANELs".  Progress is definitely being made.  But it is piecemeal and in my opinion we must still keep up the fight for meetings and conferences to better reflect the diversity of people doing interesting and important work that should be heard.  I am sure many fields still are seeing slow progress in this area but one that frustrates me personally is the microbiome arena.  So today I am coining a new term - YAMMMM (note the extra M).  Yet Another Mostly Male Microbiome Meeting.

I decided to update my mini image about this so I went to world and entered some common male names and some numbers for them.

Charles: 10
Robert: 20
Joseph: 20
David: 5
Doug: 20
Michael: 5
James: 20
William: 10
Jake: 5
Sam: 5
Richard: 10
Chris: 20
Paul: 5
Mark: 5
Donald: 10
Brian: 5
Kevin: 10
Edward: 10
Timothy: 15

And Voila:

I then added a little header

So if you see a YAMMMM - please feel free to use this image.

Saturday, March 03, 2018

Calling all academics - help improve the value of acknowledgements sections by adding ORCID IDs of people you acknowledge

UPDATE 4/4 2018.  See embedded Twitter Moment at the end of this post for, well, some issues.

I have been thinking a lot about Acknowledgement sections for papers over the last few years. One aspect of this is that I am trying to do a better job about acknowledging all the various people and agencies that provided some type of assistance for papers of mine.  I don't always do a good job of this, but I am trying to do better.  And in thinking about doing this I wondered if there was any easy way to track and quantify and make use of information in Acknowledgements.

Now, I am not an information science person or a bibliometrics person so I am not really sure how much effort there has been in tracking contributions in Acknowledgement sections but I have noticed one thing that makes this hard to do.  Some Acknowledgement sections use only initials of people when they are recognized.  Others use full names but names can be ambiguous.  But there is a better way.  If, when people thank someone in the Acknowledgements, they include a person's ORCID ID, then we have a way of tracking the recognition that people are being given.

So I decided to do this.  In a recent paper we published in PeerJ:
Hampton-Marcell JT, Gilbert JA, Eisen JA. (2017) A microbial survey of the International Space Station (ISS) PeerJ 5:e4029

We thanked five people
The authors would like to thank Summer Williams for the inception of the idea to get Science Cheerleader involved in space research. In addition we give thanks to Carl Carruthers at Nanoracks LLC for managing our space payload. We are also grateful to Holly Menninger and Rob Dunn for sharing data from the Wildlife of Our Homes pilot project, and Steven Kimball ( for publishing the original version of Fig. 7 in an open access journal, as well as sharing the underlying data.
I could not find ORCID IDs for four of them, but for one, Steven Kembel, I could.  Alas, when the article was first published, Steven's name was spelled wrong and the ORCID link was a bit messed up.  Fortunately, we needed to publish a correction to the article for some issues in the use of some terminology and due to some other parts where some editing errors existed.  And just a few days ago the correction was published.

Now the Acknowledgements read:

The authors would like to thank Summer Williams for the inception of the idea to get Science Cheerleader involved in space research. In addition we give thanks to Carl Carruthers at Nanoracks LLC for managing our space payload. We are also grateful to Holly Menninger and Rob Dunn for sharing data from the Wildlife of Our Homes pilot project, and Steven Kembel (ORCID ID: 0000-0001-5224-0952) for publishing the original version of Fig. 7 in an open access journal, as well as sharing the underlying data.

There is no longer a link to ORCID (not sure why) but that is OK - at least the ID is there.

Also I convinced a friend and colleague Raquel Peixoto to add my ORCID ID in an Acknowledgment section in a paper of hers:
We thank Jonathan A. Eisen, ORCID ID 0000-0002-0159-2197, and Alexandre Rosado for their helpful comments to improve the manuscript.
I call on the broader community to do this as much as possible for Acknowledgement sections because then it will be easier to actually connect Acknowledgements to people.


So then I posted this post.  And some people liked it.  And others, well, did not.  And, well, I made a summary of some of the response in a Twitter moment.

Sunday, February 25, 2018

Buzzfeed sadly promoting #FakeScience of Colon Cleansing

I am sorry but why in the ever living $*#(@# is Buzzfeed thinking here.

A 1st year PhD student at UC Davis Will Louie, who rotated in my lab earlier this year, sent this video around to me and the rest of my lab justifiably expressing concern over it.  And he is dead right - this is stunningly bad stuff from Buzzfeed.

The video promotes Colon Hydrotherapy as though it is a wonderful perfect treatment.  For example there is a part where it claims some of the benefits of this include speeding up metabolism, increased energy, improved digestion and more.

Later on they make the claim that it helps people lost weight too.  And no mention anywhere of any risks.  Well, that is a problem because benefits of this have not been shown scientifically and risks are known.  See for example:

Colonic irrigation: therapeutic claims by professional organisations, a review - Ernst - 2010 - International Journal of Clinical Practice - Wiley Online Library

From this paper:

Colonic irrigation is a popular treatment promoted for a wide range of conditions. The aim of this analysis is to evaluate the therapeutic claims made by professional organisations of colonic irrigation. Six such organisations were identified. On their websites, a plethora of therapeutic claims were made. Common themes were detoxification, normalisation of intestinal function, treatment of inflammatory bowel disease and weight loss. None of these claims seemed to be supported by sound evidence. It is concluded that the therapeutic claims of professional organisations of colonic irrigation mislead patients.

And also the Mayo Clinic page "Is colon cleansing a good way to eliminate toxins from your body?". Some quotes from this page are below:

Proponents of colon cleansing believe that toxins from your gastrointestinal tract can cause a variety of health problems, such as arthritis, allergies and asthma. They believe that colon cleansing improves health by removing toxins, boosting your energy and enhancing your immune system. However, there's no evidence that colon cleansing produces these effects.

And colon cleansing can sometimes be harmful. In fact, coffee enemas sometimes used in colon cleansing have been linked to several deaths. Colon cleansing can also cause less serious side effects, such as cramping, bloating, nausea and vomiting.

Other concerns with colon cleansing are that it can:
  • Increase your risk of dehydration
  • Lead to bowel perforations
  • Increase the risk of infection
  • Cause changes in your electrolytes, which can be dangerous if you have kidney or heart disease or other health problems
I mean, if you want to do colon cleansing that is your business I suppose.  But presenting a misleading video promoting it with fake science and no caveats.  Not cool Buzzfeed.

What is next for Buzzfeed?  Are they going to do a video with Gwyneth Paltrow on the benefits of vaginal eggs? And don't even get me started on the pressure points in your foot for treating your liver part of the video. Truly disgraceful Buzzfeed.

Saturday, February 03, 2018

FEBS Letters Blames Society and History for their Sexist Meeting ... #Boycott

What a joke.

I was pointed on Twitter to a meeting run by FEBS Letters to "celebrate" their 50th Anniversary.  The meeting has some 20 speakers highlighted of which only one is a woman.

See for example

And I guess in response to criticism they now write

We acknowledge that it is disappointing that there is currently only one female speaker in our line up. The FEBS Letters editorial team based its speaker selection on authors of some of the best papers published in FEBS Letters over the past 50 years, based on citations and downloads. Unfortunately, women are strongly underrepresented in this list, as a result of the fact that women in science were few over the last century. In addition, other women invited to speak at the event were not able to accept the invitation. The result below is thus currently a historical and social reflection of the past 50 years. FEBS Letters is looking at ways to address this.
That is right - for their own meeting they are blaming history and society.  How about this.  How about you take some $#$*()!@#()$!@ responsibility for the meeting you are running rather than blaming society and history for your lack of diversity?  And how about this - I call for a boycott of this meeting. Nobody should help them celebrate when this is their approach.

UPDATE - made a Twitter Moment with various Tweets on the topic