Monday, November 13, 2017

Of possible interest: Science-Corps "to teach science to underserved students and build science capacity globally. "

Just got an announcement about this from a colleague and thought it might be of interest:



Science-Corps

Providing an opportunity for recent PhD graduates, as Science-Corps Fellows, to teach science to underserved students and build science capacity in the developing world
Finished, or finishing your PhD in a science, technology, engineering, or math (STEM) field? Interested in taking a six-month break from the research/academic track to work in a different part of the world and share your expertise where it is needed? Science-Corps has launched a new fellowship, which provides STEM PhD graduates the opportunity to teach science, design curriculum, and build scientific capacity abroad.

Science-Corps is recruiting STEM PhD students near completion and up to four years post degree completion for placement starting June of 2018. Applications are due by January 31, 2018.


If interested, visit science-corps.org


Great episode of "I Contain Multitudes" on Symbioses in Hydrothermal Vents

Love this - featuring Colleen Cavanaugh - the person who got me into microbiology ...


 


 Note - I have been a scientific consultant to this project.

Monday, October 30, 2017

Storify of #UCDmicroBOOmes Halloween Symposium at #UCDavis on #microbiomes

YAMMM alert: Yet another mostly male meeting - Frontiers in Microscopy at Janelia Farm

So I got invited to a meeting at Janelia Farm today. Alas I cannot go because it is while I am teaching in the Spring. But in pondering the meeting (which is not posted currently on the Janelia site) I decided to snoop around and see what their other meetings looked like. And, as I generally do, I also scanned the meetings to see if they seemed to have diverse participant pools. And, well, the first meeting on their Spring meeting list alas did not look so good from a diversity point of view.
This is the meeting: Frontiers in Microscopy Technologies and Strategies for Bioimaging Centers Network
This unique meeting will bring together directors of imaging centers and program leaders of open access infrastructures. Our goal is to create a platform to explore the frontiers in imaging technologies, discuss common challenges, and strategize how the global imaging community can build a common network to tackle the era of “big data” as well as rapid technological advances in microscopy.
First glance did not look great so I dug into it a bit more. I tried to infer the gender of the people listed on the site by looking for their personal web sites or other descriptions of them to see what gender pronouns were used. When that was not available I guessed based on name or appearance. I know this is not ideal / perfect but it usually does a decent job of estimating gender balance for a meeting.

Here is what I inferred (and color coded). 
  • Male
  • Female

Organizers
  1. Teng-Leong ChewJanelia Research Campus/HHMI 
  2. Antje Keppler, European Molecular Biology Laboratory 

Ok that is good. It has been shown that having a good gender balance of organizers can help lead to a good balance for a meeting. 

Invited Participants
  1. Holly Aaron, University of California, Berkeley
  2. Pablo Ariel, University of North Carolina at Chapel Hill
  3. Richard Cole, NY State Department of Health, Wadsworth Center
  4. Hunter Elliott, Harvard Medical School
  5. John Eriksson, Turku BioImaging
  6. Scott Fraser, University of Southern California
  7. Jeremy Freeman, Chan Zuckerberg Initiative
  8. Ronald Germain, National Institute of Allergy and Infectious Diseases/NIH
  9. Gary Greenburg, Gordon and Betty Moore Foundation
  10. David HoffmanJanelia Research Campus/HHMI
  11. James Jonkman, Advanced Optical Microscopy Facility
  12. Luke Lavis, Janelia Research Campus/HHMI
  13. Jennifer Lippincott-SchwartzJanelia Research Campus/HHMI
  14. Elisa May, University of Konstanz
  15. Robert Price, University of South Carolina
  16. Joshua Rappoport, Northwestern University
  17. Jean Salamero, Institut Curie
  18. Hari Shroff, National Institute of Biomedical Imaging and Bioengineering/NIH
  19. Robert Singer, Albert Einstein College of Medicine
  20. Jason Swedlow, University of Dundee
  21. Aaron TaylorJanelia Research Campus/HHMI
  22. Paul Tillberg, Janelia Research Campus/HHMI
  23. Jean-Yves Tinevez, Institut Pasteur
  24. Michael Unser, École Polytechnique Fédérale de Lausanne
  25. Jennifer Waters, Harvard Medical School
  26. Simon Watkins, University of Pittsburgh
Well, this is pretty skewed.  That comes to 22:4 male; female.

Or 85% male.

The meeting I was invited to had a pretty good gender balance of invited participants.  So maybe this microscopy meeting is an anomaly.  But it made me wonder - does HHMI or Janelia Farm haver a diversity policy for meetings?  I could not find anything in Googling around or looking at their web sites.  If they do not have one, I think they should consider developing one.  I did find many examples of what seems to be a commitment to supporting diversity in STEM by HHMI.  But this meeting is definitely not doing a good job of that.  HHMI can do better.


Thursday, October 26, 2017

Really excellent article on "Imagining the Open University" by Erin McKiernan

This is definitely worth a look:



Imagining the “open” university: Sharing scholarship to improve research and education



Abstract



Open scholarship, such as the sharing of articles, code, data, and educational resources, has the potential to improve university research and education as well as increase the impact universities can have beyond their own walls. To support this perspective, I present evidence from case studies, published literature, and personal experiences as a practicing open scholar. I describe some of the challenges inherent to practicing open scholarship and some of the tensions created by incompatibilities between institutional policies and personal practice. To address this, I propose several concrete actions universities could take to support open scholarship and outline ways in which such initiatives could benefit the public as well as institutions. Importantly, I do not think most of these actions would require new funding but rather a redistribution of existing funds and a rewriting of internal policies to better align with university missions of knowledge dissemination and societal impact.

Sunday, October 15, 2017

From Google Scholar: Follow Related Research for Key Authors

This seems like it could be useful:



Google Scholar Blog: Follow Related Research for Key Authors


Scholar provides several ways to keep up with research in your area. You can set up keyword alerts, get recommendations related to your publications and follow your colleagues’ profiles.

Today, we are adding another approach to stay up to date in areas of your interest. Now, in addition to following articles by and citations to an author, you can follow research that is related to her work. 
To follow related research for an author, simply go to her public profile, click “Follow” and select “New articles related to this author’s research”. Scholar will automatically scan all new publications for articles related to her research and will send them to you as an email alert. 
This is particularly useful if you are a graduate student or an early stage researcher. By following related research for your advisor, your thesis committee and possibly a few key faculty members in your department, you would be able to see the research landscape from their experienced vantage point.

It is also useful if, like myself, you are an industry or medical professional who isn’t active in the research realm but would like to keep up. By following related research for leading scholars, you will be able to quickly view relevant articles in key areas.
The astute reader has no doubt guessed that this can also be used to get email alerts for research related to your own work -- go to your public profile, click “Follow” and select “Recommended articles”.

Monday, October 09, 2017

Offensive overselling of the #microbiome in breast cancer from the Cleveland Clinic





This is just sickening to me.

I saw a news story that smelled funny:  Breast cancer: Bacterial deficiency linked with onset. And I went and found the scientific paper and then the press release from the Cleveland Clinic that the news story seemed based on.  And, well, the press release turns out to be ridiculous.

The paper showed something somewhat interesting but very limited.  Here is the abstract with key parts bolded and underlined by me
It has long been proposed that the gut microbiome contributes to breast carcinogenesis by modifying systemic estrogen levels. This is often cited as a possible mechanism linking breast cancer and high-fat, low-fiber diets as well as antibiotic exposure, associations previously identified in population-based studies. More recently, a distinct microbiome has been identified within breast milk and tissue, but few studies have characterized differences in the breast tissue microbiota of patients with and without cancer, and none have investigated distant body-site microbiomes outside of the gut. We hypothesize that cancerous breast tissue is associated with a microbiomic profile distinct from that of benign breast tissue, and that microbiomes of more distant sites, the oral cavity and urinary tract, will reflect dysbiosis as well. Fifty-seven women with invasive breast cancer undergoing mastectomy and 21 healthy women undergoing cosmetic breast surgery were enrolled. The bacterial 16S rRNA gene was amplified from urine, oral rinse and surgically collected breast tissue, sequenced, and processed through a QIIME-based bioinformatics pipeline. Cancer patient breast tissue microbiomes clustered significantly differently from non-cancer patients (p=0.03), largely driven by decreased relative abundance of Methylobacterium in cancer patients (median 0.10 vs. 0.24, p=0.03). There were no significant differences in oral rinse samples. Differences in urinary microbiomes were largely explained by menopausal status, with peri/postmenopausal women showing decreased levels of Lactobacillus. Independent of menopausal status, however, cancer patients had increased levels of gram-positive organisms including Corynebacterium (p<0.01), Staphylococcus (p=0.02), Actinomyces (p<0.01), and Propionibacteriaceae (p<0.01). Our observations suggest that the local breast microbiota differ in patients with and without breast cancer. Cancer patient urinary microbiomes were characterized by increased levels of gram-positive organisms in this study, but need to be further studied in larger cohorts.
That is it.  Barely significant finding of some clustering of the microbiomes of breast cancer patients versus those of patients without breast cancer.  And yet, this turned in the press release into cancer causing bacteria that they will be fighting with nanotechnology.  Seriously.

The press release title and subtitle is semi OK:
Cleveland Clinic Researchers Find Link Between Bacterial Imbalances and Breast Cancer. Study compares bacterial composition in healthy vs. cancerous breast tissue
But it goes way way way downhill from there.  Here are the parts with problems
  •  In our wildest dreams, we hope we can use microbiomics right before breast cancer forms and then prevent cancer with probiotics or antibiotics
    • Sure, in my wildest dreams I would cure cancer too.  
  • In addition to the Methylobacterium finding, the team discovered that cancer patients’ urine samples had increased levels of gram-positive bacteria, including Staphylococcus and Actinomyces. Further studies are needed to determine the role these organisms may play in breast cancer.
    • Umm.  No. Further studies are needed to see if these organisms play ANY role of any kind in breast cancer.
  • Co-senior author Stephen Grobymer, M.D., said, “If we can target specific pro-cancer bacteria, we may be able to make the environment less hospitable to cancer and enhance existing treatments. Larger studies are needed but this work is a solid first step in better understanding the significant role of bacterial imbalances in breast cancer.
    • Noooooooooooooooooooooooooooo.  You have not shown anywhere that there are "pro cancer" bacteria and this quote clearly implies that you have. 
  • The study provides proof-of-principle evidence to support further research into the creation and utilization of loaded submicroscopic particles (nanoparticles), targeting these pro-cancer bacteria. 
    • What?  This study does not provide ANY proof of principle of this sort.  You have not shown there are any pro-cancer bacteria.  This is ridiculous and offensive.  
No wonder the news stories imply that this study is about preventing breast cancer.  The press release from the Cleveland Clinic is deceptive.  It makes claims about the work that are irresponsible, misleading, and potentially dangerous. The Cleveland Clinic should be ashamed.

And thus the Cleveland Clinic is the winner of this edition of the Overselling the Microbiome Award.


UPDATE 10/16/17

And so the deceptive PR from Cleveland Clinic is now leading to claims of "Antibiotics May Prevent Breast Cancer" See


Friday, October 06, 2017

This week in Science SPAM

I would love it if I could just ignore my Gmail Spam folder.  Alas, every once in a while I find important emails in Gmail Spam.   So alas I cannot ignore it. While digging through today I found a collection of "Science Spam" - that is Spam emails that have some science-y theme.

Here are the ones from this week in my Gmail Spam folder that I identified as being Science Spam.   Most are invites from Spammy journals.  Some are invites from Spammy conferences.  A few are other things.  Do other people get this much science Spam?






Monday, September 25, 2017

Nature Publishing Group continues to deceive about #OpenAccess to genome papers

I was reminded today about the wonderful history of Nature in it's claim that it would make all papers reporting a new genome sequence freely and openly available. I wrote about how this was, well, not the truth, in 2012: The Tree of Life: Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh. And today I decided to recheck this.

So I searched for "Genome sequence" on the Nature site

And, well, I found a doozy of an example of a paper that is supposed to be openly available but is not. Initial sequencing and analysis of the human genome



That's right.  The "public" human genome paper is not freely or openly available.  It is $4.99 to rent or $20 to purchase.  Is this Nature's way of saying "We think the Lander et al. paper did not actually report on a genome?" and that the Venter paper truly won the race?  I don't think so.  I think this is a way of Nature saying "How can we make money off of our past papers? Which one gets a lot of looks? What? It is freely available? Change that." or something like that.

Want to bet they will say this is a mistake?  Want to bet they will not refund anybody's money who paid for this?

Here is a simple solution for everyone out there.  Do not trust Nature Publishing Group to make something available even if they say they will.


UPDATE 9/25 1 PM

But wait - there is more.  The Plasmodium genome paper, which I wrote about in 2012 not being available and which Nature promised to fix is again behind a pay wall










And more



UPDATE 10/16/17

Nature has apologized and said they fixed the issue and will refund any money people spent to buy these articles



Friday, September 01, 2017

Trip to Chaa Creek Lodge in Belize - Day 1

Note - writing this with some help from my daughter.

My family and I went on a trip to Belize in early August 2017 and I am posting some notes and pictures from the trip here.

We chose Belize for a few semi - random reasons.  First, we had wanted to go to Europe but we really only could travel just the week before school started for my kids and we felt like Europe was (1) too far (2) would involve too much jet lag and (3) would involve too many Real Madrid fans.  So we started looking around closer to home.  We wanted to go out of the country (out of the USA - not just out of California, though it really is it's own country).  So - well - we looked at Mexico.  And Central America.  And we settled on Belize.

We decided to spend the whole week of our trip at one place and, since we have been going to Hawaii a bit recently, we decided we did not want to spend our time in a beach-like setting, so we looked for places in the inland rainforesty areas.  My wife spent quite a lot of time searching for possible places and she came up with some candidates and after discussions on the pluses and minuses of all the places and after also asking Twitter and friends and such we settled on Chaa Creek.  An ecolodge of sorts with a slight upscale angle.

More on the place and such later.

Right now I really want to start to get some pictures posted.  So here are some from our travel day.

SMF to Dallas to Belize.

On the plane
I did not take too many (well, more than one) pictures on the actual trip.  But suffice it to say we flew on a plane.


An interesting shirt at a shop at the airport

Waiting for our ride while all the local taxi drivers, well, tried to offer us rides in ways I found to be, well, dubious. 

The ride to Chaa Creek was about two hours long.  I took some pics along the way.  Here are some of them.  Oh - and our driver, Edward, was an FC Barcelona fan.  Yay.

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek 
On the road to Chaa Creek 
On the road to Chaa Creek 
Off to the reception building 
Off to the reception building

Off to the reception building

Off to the reception building

We settled in, got some dinner, and were very hot.  Like really very hot.  Like really really warmer than warm.  It was beautiful.  And interesting.  And hot.  Really really hot.  Or, more relevant.  It was hot and really really humid.  I mean, I grew up in the Washington DC area so I know hot and humid.  But I live in California now, where hot and humid usually do not go together.  We get hot in Davis.  Really really really hot.  But dry. Like really really dry. .


Saturday, August 26, 2017

Crosspost: Everyone should read this piece by Ed Yong: Norm Pace Blew The Door Off The Microbial World – microBEnet: the microbiology of the Built Environment network

Crosspost: just pointing people to this post I wrote on microBEnet which may be of interest:

Everyone should read this piece by Ed Yong: Norm Pace Blew The Door Off The Microbial World – microBEnet: the microbiology of the Built Environment network

Crosspost: #MoBE17: Microbiology of the Built Environment Research & Applications Symposium – microBEnet: the microbiology of the Built Environment network

Crossposting from microBEnet



#MoBE17: Microbiology of the Built Environment Research & Applications Symposium – microBEnet: the microbiology of the Built Environment network

This meeting should be of interest to many out there. A great collection of speakers and topics. Keynotes by Ed Yong, Susan Lynch and Marc Edwards. Registration deadline is September 1.



MoBE 2017
Microbiology of the Built Environment
Research and Applications Symposium
October 10 - October 12, 2017
NAS Building Washington, DC


More detail here.

Registration is free and open until September 1, 2017.

Sponsors Include: Alfred P. Sloan Foundation, NAS, Zymo Corporation, Standards in Genomics Sciences, Microbiome Journal, NASA, US Green Buildings Council




Agenda

Tuesday October 10th
Keynote.
  • Ed Yong (The Atlantic). A science writer’s view of the MoBE field.
Kick-off reception 


Wednesday October 11th
Introduction
  • Lynn M. Schriml (MoBE 2017 symposium chairman, University of Maryland School of Medicine, Institute for Genome Sciences)
  • Paula J. Olsiewski (MoBE Program Director, Alfred P. Sloan Foundation)
Keynote
  • Susan Lynch (UCSF School of Medicine). Chronic Inflammatory Disease and the Built Environment
Session 1: MoBE Science Here and Now
  • Jonathan Eisen (UC Davis). The microbiology of the built environment network (microBEnet) and perspectives on the MoBE field
  • Jessica Green (University of Oregon). Designing healthier spaces and buildings
  • Lisa Brenner (University of Colorado). Mental Health and the Microbiome of the Build Environment
Session 2: Implications of MoBE for Health and Design
  • Elaine Hubal (EPA). Session Chair
  • Shelly Miller (University of Colorado). Building Engineering Controls for Improving Occupant Health: Mitigating Airborne Particles, Toxic Gases, and Infectious Aerosols.
  • Rachel Adams (BIMERC). Sources and quantities of microbes and mVOCs indoors.
  • Karen Dannemiller (Ohio State University). The nexus of housing characteristics, indoor microbial communities, and asthma severity
  • Mark Mendell (California Department of Health, LBNL). Adverse and beneficial effects of the indoor microbiome – current implications for health or design?
Session 3: Public Health and Indoor Microbial Communities
  • Diane Gold, Session Chair
  • Maria Gloria Dominguez-Bello (NYU School of Medicine). Microbial Biogeography of Homes across urbanization gradients
  • Brandon Bubba Brooks (Kaleido Biosciences). The NICU microbiome’s role in neonate gut colonization
  • Jane Carlton (NYU School of Medicine). A city view: ATM's, parasites and wastewater
Session 4: MoBE Insights on Microbial Exposure
  • Tina Bahadori (EPA) Chemical Safety for Sustainability Research Program Leader, Session Chair
  • Eric Alm (MIT). Sewers, microbes and drugs
  • Emmanuel Mongodin (Institute for Genome Sciences, UMSOM). Microbial function and built environments
  • David Mills (UC Davis). Microbiology of food production built environments: dairies and wineries
Panel Discussion: Myth and Reality of MoBE Manipulation
  • Rob Knight (UCSD), Moderator
  • Rita Colwell (University of Maryland)
  • Jeffrey Siegel (U of T)
  • Ilana Brito (Cornell)
  • Jessica Green (University of Oregon)
Poster Session & Reception



Thursday October 12th
Welcome
  • Jordan Peccia (Yale). Gordon Conference Announcement.
Keynote
  • Marc Edwards (Virginia Tech). MoBE, Public Health and the Flint Water Crisis
Session 5 - From MoBE Research to MoBE Applications
  • Scott Kelley (San Diego State University). Session Chair.
  • Jack Gilbert (University of Chicago). From Hospitals to Forensic Applications
  • Richard Shaughnessy (University of Tulsa). From Home to School: Tribal Indoor Air Quality Intervention Study
  • Anders Benteson Nygaard (Oslo and Akershus University College of Applied Sciences). Bacteria in Norwegian kindergartens: Small children and their microbial environments
Session 6: The Building Science – MoBE nexus
  • Richard Corsi (University of Texas at Austin). Session Chair.
  • Richard Corsi (University of Texas at Austin). Building Science ∩ Science in Buildings (or why MoBE > Robots)
  • Amy Pruden (Virginia Tech). Towards Prebiotic/Probiotic Control of the Microbiome in Built Water Systems
  • Betsy Pugel (NASA). Tiny houses: Planetary protection-focused materials selection for spaceflight hardware surfaces
  • Kent Duffy (SRG Partnership). The influences of microbial research on architectural practice
  • Wendy J Goodson (Air Force Research Laboratory). Microbiomes of Military Cargo Aircraft and their Connection to Biocorrosion
Session 7 - NAS Microbiomes of the Built Environment Consensus Study
  • Katherine Bowman (NAS). Session Chair.
  • Joan Bennett (Rutgers University) : NAS MoBE study overview MoBE outcomes, perspectives and future studies
Panel Discussion: Charting MoBE Research Priorities
  • Jonathan Eisen (UC Davis). Moderator.
  • Jordan Peccia (Yale)
  • Norman Pace (University of Colorado)
  • Claire Fraser (Institute for Genome Sciences, UMSOM)
Meeting Closing
  • Paula Olsiewski (Alfred P. Sloan Foundation).

Wednesday, August 09, 2017

The Massry Prize is a #YAMMA (yet another mostly male award) #MatildaEffect #Massry #GenderBias

I was really pleased to see the announcement that the 2017 Massry Prize was awarded to Norm Pace, Jeffrey Gordon and Rob Knight.  Alas, then someone pointed me to the web site listing past winners of the prize. Massry Prize.  And I compiled the list (with some help from Wikipedia)

Massry Prize
Yet Another Mostly Male Award
YAMMA
  1. 1996 Michael Berridge 
  2. 1997 Judah Folkman 
  3. 1998 Mark Ptashne 
  4. 1999 Gunter Blobel 
  5. 2000 Leland H. Hartwell 
  6. 2001 Avram Hershko
  7. 2001 Alexander Varshavsky 
  8. 2002 Mario Capecchi
  9. 2002 Oliver Smithies 
  10. 2003 Roger Kornberg
  11. 2003 David Allis 
  12. 2003 Michael Grunstein 
  13. 2004 Ada Yonath 
  14. 2004 Harry Noller 
  15. 2005 Andrew Fire
  16. 2004 Craig Mello 
  17. 2004 David Baulcombe 
  18. 2006 Akira Endo
  19. 2007 Michael Phelps 
  20. 2008 Shinya Yamanaka
  21. 2008 James A. Thomson
  22. 2008 Rudolf Jaenisch 
  23. 2009 Gary Ruvkun
  24. 2009 Victor Ambros 
  25. 2010 Randy Schekman 
  26. 2011 F. Ulrich Hartl 
  27. 2011 Arthur Horwich
  28. 2012 Michael Rosbash
  29. 2012 Jeffrey C. Hall
  30. 2012 Michael W. Young 
  31. 2013 Michael Sheetz
  32. 2013 James A. Spudich 
  33. 2013 Ronald D. Vale 
  34. 2014 Steven Rosenberg
  35. 2014 Zelig Eshhar 
  36. 2014 James P. Allison
  37. 2015 Philippe Horvath
  38. 2015 Jennifer Doudna 
  39. 2015 Emmanuelle Charpentier
  40. 2016 Gero Miesenböck
  41. 2016 Peter Hegemann
  42. 2016 Karl Deisseroth
  43. 2017 Rob Knight
  44. 2017 Jeff Gordon
  45. 2017 Norm Pace
42 male
3 female

I colored them based on my inference of gender. I realize that I may have some of this wrong and that using a binary system is not right in many cases but I think this certainly shows a pattern.  I also realize there are many possible explanations for the imbalance here but I think it is reasonable to consider that bias against women may be a component of this. 

Some useful reading in regard to prizes in the sciences:
Not sure what to do here with this information.  I deeply respect the award winners here and think they are highly deserving of important science awards.  But it pains me to see such a big skew in the gender balance of winners of this Massry Prize and think, sadly, that there is likely some kind of bias at work here.  When there is a bias against recognizing the achievements of women it is known as the Matilda Effect.  I suggest everyone involved in handing out awards such as this, and anyone reporting on such awards, should read up on it.

I note - I posted the gender ratio of winners of this award to the Gender Avenger site. See below:

Thursday, August 03, 2017

#SciFoo 2017 here I come

Well, I am going back to SciFoo. This is a meeting that happens at Google, is organized by O'Reilly Media and Nature and Google and Digital Science and others.  I went in 2012, 2007 and 2006.  And every single time it was life altering.  I will try to post while there but it can be distracting ...Here are some notes and posts from the past scifoos I have attended.

2012

Storify I made:

Monday, July 24, 2017

Another white men's microbiome meeting from Kisaco #YAMMM #manel #STEMDiversity

Well, this is really unpleasant.

Last year I blogged about a what I called "The White Men's Microbiome Congress." The gender balance of the meeting was so bad I called for a boycott. And my call seemed to have some impact as many people refused to participate and then the meeting organizers from Kisaco Research responded, apologized for the gender bias, and made some attempts to at least try to fix things. For example they posted on my blog:
We recognize that it is our responsibility to help ensure that the speaker faculty reflect the diversity and culture of the field and science as a whole. In this instance we failed to live up to our own standards of sensitivity and diversity, for which we sincerely apologize. Kisaco Research is deeply committed to producing events that represent the diversity of the scientific fields we work with. We are embarrassed that this has been previously overlooked and are currently working to make this, and all other programmes, ones that the top scientists are proud to be a part of. 
And they did seem to try to make the meeting I critiqued less biased.

And thus it was really disturbing to me when someone sent me the invite they received to a microbiome meeting organized by this group and pointed out that it had the same issue. I went to the web site for this new meeting - the "3rd annual European microbiome congress (see The Microbiome Congress – Europe – Kisaco Research). And it confirmed my fears.



95% of the highlighted speakers are male (as always, I note, assessing the gender balance of a meeting is not always straight forward.  In this case I looked at the web sites of the speakers and other descriptions of them to see what pronouns were used to describe them.  I think my assessment is accurate but I apologize if I made mistakes). And all of them appear to be white.  It is a meeting for white men to speak at.  The field of microbiome studies is rich and diverse in many ways - including in the scientists and others who work on the topic.  It would not have been hard to come up with a more diverse set of speakers.  In fact, the field is so diverse in terms of researchers that I think this speaker line up - especially in light of the previous meeting - is evidence for bias.   I am not sure where that bias comes in (it could be at invitations, at acceptances, or other places) but it is pretty clear this is not a random selection of top microbiome researchers.

As this is a pattern from Kisaco Research I am calling for the following
  • People should boycott this meeting. That is, do not attend this meeting.
  • People should Boycott all Kisaco meetings. This is a pattern for Kisaco, and not a good one.  Nobody should attend any of their meetings
  • The meeting sponsors should withdraw support for this meeting. The listed sponsors include Synthetic BiologicQiagenProDigestAffymetrix and Zymo Research. I encourage people to contact them about this and pressure them to rescind their sponsorship.  I have already contacted Zymo, for which I am an advisor.  I will let people know how they respond. 
  • The speakers should cancel their participation.  A meeting cannot go on without the speakers. The listed speakers include:
Of course, it would be better to prevent such things from happening in the future.  Some things to consider that will start to shift away from meetings with poor diversity of presenters:
  • Make diversity of presenters one of the factors you consider when deciding whether or not to accept invitations to speak at or attend a meeting. Some ways to make an informed decision here include
    • looking at past meetings by the same organizers
    • asking for a list of presenters for the meeting one is invited to
    • asking if the meeting has any policies on diversity
  • When you are involved in organizing a meeting work to make it a stellar meeting that also happens to have a diverse collection of presenters (diverse in background,  race and ethnicity, kills, perspectives, gender, types of institutions, careers stages, country of origin, and more). 
  • Develop diversity policies for meetings in which you are involved
  • If you are on the sponsorship side of things - require meeting organizers to have a diversity policy and to show their prior track records before you offer support
  • Develop and support practices and policies that would help make meetings more diverse 

Also check out some of these articles and posts

It is entirely possible to run meetings where there is no bias against particular groups in the presenter line up.  It is also possible to embrace diversity and all of its benefits and make a meeting that is simply better than a meeting where diversity is not embraced.  It does take some effort.  But it is worth it.

UPDATE. Making a Storify of some responses



Saturday, July 22, 2017

Today in misleading, dangerous, overselling of the microbiome - UNC on babies and cognitive development


Uggh. Was pointed to this on Twitter:

In baby's dirty diapers, the clues to baby's brain development | EurekAlert! Science News

And I read the PR and made a quick Twitter response but decided to fill that in here a bit.
Basically the study being discussed found a correlation between the microbiome in babies poop and their cognitive development. There are 100s of possible causes for such a correlation. But the press release misleading went on about how their work suggests they maybe able to somehow intervene to guide development by manipulating the microbiome. Ridiculous.

Here are some problematic quotes


  • "In baby's dirty diapers, the clues to baby's brain development"
    • Not really any clues providing in this work towards brain development. They have an interesting observation. It is unclear if it provides any insight into brain development.
  • Findings from the UNC School of Medicine shed light on the surprising role of bacteria in how our brains develop during the first years of life
    • No no no no no and no. They do not show ANY role of bacteria in how brains develop.
  • Our work suggests that an 'optimal' microbiome for cognitive and psychiatric outcomes may be different than an 'optimal' microbiome for other outcomes."
    • Oh #FFS. They do not show in any way what is or is not an "optimal" micro biome. They have a $*(#($# correlation. That is it.
  • Though the findings are preliminary, they suggest that early intervention may hold the key to optimizing cognitive development.
    • Well sure if you use the term "may" generously here they may hold such a key. But if you want to use it generously then these results may also suggest that UNC may be a dangerous place to bring babies because some of them may get a defective microbiome there which may lead them to have cognitive problems. You see, the findings in this work actually do not really suggest anything about early intervention at this point. Ridiculous to even suggest it.
  • One was that when measuring the microbiome at age one, we already see the emergence of adult-like gut microbiome communities -- which means that the ideal time for intervention would be before age 1."
    • No not really. Even if intervention was actually indicated here (which again, it is not) this does not mean that the time to intervene can be determined by looking at where they get an "adult" like micro biome. Because they have no mechanism here. It could be something in the baby and adult microbiome that is doing this (again, assuming there is a causal connection which there is not one shred of evidence for).

And then this is the worst.
"Big picture: these results suggest you may be able to guide the development of the microbiome to optimize cognitive development or reduce the risk for disorders like autism which can include problems with cognition and language," said Knickmeyer. "How you guide that development is an open question because we have to understand what the individual's microbiome is and how to shift it. And this is something the scientific community is just beginning to work on."
What the living #$*@(#(@? Now they are suggesting that their results say you may be able to optimize cognitive development and reduce the risk of autism. All from a simple correlation for which they have no clue whether there is any mechanistic connection. Offensive. Dangerous. Ridiculous. Sad.