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