Eisen Lab Blog

Time to boycott Oxford Global meetings due to blatant sexism

I don’t even know what to say or do about this it is so stunningly pathetic.  I saw this Tweet earlier in the day:

I figured even in an era of blatant sexism in science, this must be a mistake right?  How could there be a conference with 38 male speakers and 0 female speakers.  So I went to the site: Who is Speaking – Oxford Global’s 13th Pharmaceutical IT Congress, September 2015.  And, well, as far as I can tell Elisabeth Bik has the numbers right.  (See a list at the end of this post).  They even have a running slideshow of the speakers faces.

This is even worse than the 25:1 ratio of the qBio meeting I lost it over a few years ago.  I have never seen anything like this. I note – a 38:0 ratio is nearly impossible by chance in any field and I think pretty clearly an indication of massive bias of some kind.

I note – this is not the first case of a mostly male meeting from Oxford Global.  See for example:
Oxford Global Sequencing Meetings: Where MEN Tell You About Sequencing #YAMMM

I think it is time to just boycott meetings meetings from Oxford Global.  The only way they will change is if people stop speaking at or going to their meetings.  So please – stop going to their meetings.  Stop speaking at their meetings.

Speakers 2015:

  • Sebastien Lefebvre 
    Director Data Engineering and Technology – Global Data Office, Biogen Idec
  • Uwe Barlage
    EDC Project Leader, Bayer Healthcare
  • Marc Berger
    Vice President, Real World Data and Analytics, Pfizer
  • Michael Braxenthaler
    Pharma Research and Early Development Informatics, Global Head Strategic Alliances, Roche, & President, Pistoia Alliance
  • Arnaub Chatterjee
    Associate Director – Data Science, Insights and Partnerships, Merck
  • James Connelly
    Global Head, Research Data Management, Sanofi
  • Jos Echelpoels
    Director IT, Regional Initiatives, Janssen
  • Brian Ellerman
    ‎Head of Technology Scouting and Information Science Innovation, Sanofi
  • Peter Elsig Raun
    Director & Head Business Analysis, Lundbeck
  • Dimitrios Georgiopoulos
    Chief Scientific Officer UK, Novartis
  • Charles Gerrits
    Vice President, Innovative Patient-Centric Endpoints and Solutions, Sanofi
  • Yike Guo
    Professor of Computing Science, Imperial College London and Chief Technology Officer, tranSMART Foundation
  • Sergio H. Rotstein
    Director, Research Business Technology, Pfizer
  • Juergen Hammer
    Global Head Data Science, Center Head Pharma Research and Early Development Informatics, Roche
  • Jan Hauss
    Head Central Analytics Informatics, Merck
  • Athula Herath
    Statistical Director, Translational Sciences, MedImmune
  • Nigel Hughes
    Director Integrative Healthcare Informatics, Janssen Research and Development
  • Michael Hvalsøe Brinkløv
    BI Architect, IT Platforms & Infrastructure, Lundbeck
  • Robert J. Boland
    Senior Manager, Translational Informatics & External Innovation R&D IT, Janssen
  • Adrian Jones
    Associate Director, Business Intelligence Systems, Astellas
  • Srivatsan Krishnan
    Director and Head of R&D Operations and IT, Bristol-Myers Squibb
  • Philippe Marc
    Global Head of Preclinical Informatics, Novartis Institutes for Biomedical Research
  • Dermot McCaul
    Director, Preclinical Development and Biologics IT, Merck
  • Pantaleo Nacci
    Head Statistical Safety & Epidemiology/PV, Novartis Vaccine and Diagnostics Srl (a GSK company)
  • Gerhard Noelken
    Global Business IT Lead for Pharmaceutical Science, Pfizer WRD
  • Emmanuel Pham
    VP Biométrie, Ipsen 
  • Andrew Porter
    Director, Enterprise Architecture, Merck
  • Gabriele Ricci
    Vice President of TechOpps IT, Shire
  • Anthony Rowe
    Director, Translational Informatics and External Innovation, Johnson & Johnson
  • Martin Ryzl
    Director, GIC Analytics Platform Engineering, Merck
  • Wolfgang Seemann
    Senior Project Manager, Bayer Business Services
  • Aziz Sheikh
    Professor of Primary Care Research & Development and Co-Director Center for Population Health Sciences, The University of Edinburgh
  • Yan Song
    Associate Director, Bioanalysis Operations, AbbVie
  • Devry Spreitzer
    Director, Global Electronic Systems Quality Assurance, Astellas
  • Jason Swift
    Head R&D Information UK, AstraZeneca
  • Kevin Teburi
    Director – iMed Team Leader, R&D Information, AstraZeneca
  • Simon Thornber
    Director, Data Analytics, Informatics and Innovation, GlaxoSmithKline
  • Tjeerd Van Staa
    Professor of Health eResearch, University of Manchester
Some past meetings from Oxford Global to consider
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Koalas, Chlamydia, Antibiotics and Microbiomes – what else do you need?

Katie Dahlhausen, a PhD student in my lab, has become really really interested (perhaps a bit obsessed) with a really interesting case study regarding koalas, Chlamydia, antibiotics, and microbiomes.  Since we do not have funds to work on this in the lab, she has started an Indiegogo campaign to raise funds to work on this.  For more information on this project and how Koalas, Chlamydia, antibiotics and microbiomes are connected see “The Koala Project” page.

https://www.indiegogo.com/project/the-koala-project/embedded/10753031 amzn_assoc_ad_type = “contextual”; amzn_assoc_tracking_id = “thtrofli-20”; amzn_assoc_marketplace = “amazon”; amzn_assoc_region = “US”; amzn_assoc_placement = “L2CQGSJAS2J24HJX”; amzn_assoc_linkid = “L2CQGSJAS2J24HJX”; amzn_assoc_emphasize_categories = “51569011, 1000, 13900861, 13900871, 301668, 2619533011, 229534, 3375251”; amzn_assoc_fallback_products = “0879696842”; amzn_assoc_width = “400”; amzn_assoc_height = “90”; //z-na.amazon-adsystem.com/widgets/q?ServiceVersion=20070822&Operation=GetScript&ID=OneJS&WS=1&MarketPlace=US&source=ac

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Michael Fischbach at #UCDavis 5/15 noon: Insights from a global view of secondary metabolism: Small molecules from the human microbiota

FridayGBSF 1005
Noon

Dr. Michael Fischbah of UCSF
"Insights from a global view of secondary metabolism: Small molecules from the human microbiota”

5/18 at #UCDavis Hunter Fraser on “Exploring the impact of noncoding genetic variation in humans”

“Exploring the impact of noncoding genetic variation in humans”

Hundreds of genome-wide association studies (GWAS) have found that the vast majority of human genetic variation impacting complex traits occurs outside of protein-coding regions, yet our understanding of these noncoding variants is still quite poor. I will describe our recent efforts to explore the impact of these functional variants. We have developed new experimental approaches to detect which variants affect key components of transcriptional regulation such as transcription factor binding, DNA methylation, and histone modification. We are also developing new computational methods for detecting natural selection in noncoding regions, revealing a dominant role of cis-regulatory changes in recent human adaptation.

Speaker: Hunter Fraser

Assistant Professor

Stanford University

Monday, May 18, 2015

4:10-5:00 PM

1022 Life Sciences

5/13 at #UCDavis: Alex Csiszar on “The Scientific Journal: A Political History” #ICIS

Please join us for Alex Csiszar (Harvard University) speaking on "The Scientific Journal: A Political History"

Wednesday, May 13, 2015, 12:00 pm – 1:30 pm
2nd Floor Instruction Room, Shields Library

Lunch will be served – Please RSVP at this link if you plan to attend http://goo.gl/forms/4D9nm6NXps

Scientific journals are expected to do a lot of different things. They are often identified with both the cumulative and the present state of knowledge possessed by scientific communities. Journals are supposed to be public enough that any interested reader might access them; yet at the same time they are rigorously exclusive. To publish in a particular set of journals is to be deemed an expert in the corresponding scientific field. When questions arise as to what scientific consensus is on some matter of concern, governmental bodies, the public, and journalists routinely look to the reputable journal literature dealing with that subject. The list of a researcher’s papers is a unit by which careers are measured and a dominant factor in decisions about hiring, tenure, and grants. Scientific journals are both permanent archive and breaking news, both complete record and painstaking selection, both public forum and the esoteric domain of experts.

This talk will explore how and why this improbable state of affairs came into being over the course of the nineteenth century. The shift whereby the authority of science came to be vested increasingly in serialized print did not come about through any deliberate decision taken by scientists based on the fitness of the periodical press to play this role. Far from emerging out of a timeless need for a secure communications medium and format, the ascendancy of the scientific journal occurred as European scientific elites sought to establish their collective legitimacy to speak authoritatively about nature following the political upheavals of the Napoleonic Wars. Since that time, the scientific journal has been a nodal point where expert cultures of credibility have intersected, uneasily, with public criteria of accountability.

Alex Csiszar is an Assistant Professor of the History of Science at Harvard University. His research concerns the history of scientific authorship, publishing, refereeing practices, and information management from the French Revolution to the twentieth century.

9 things PBS Newshour famously gets horrible wrong in story on fast food and microbiomes

Well, this is one of the worst microbiome news stories in a long time: Fast food kills gut bacteria that can keep you slim, book claims.  So many things wrong with it I don’t even know where to go.  Here are nine:

1. The original headline: “Fast food kills gut bacteria that can keep you slim, study finds”

Here is the Tweet

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2. The correction:

is just completely lame and they should, as the New York Times does when it makes a correction, say what it used to say before they changed it

3. The sentence with the reference to Rob Knight is just bad reporting #1

Here is the quote:

Previous studies made similar findings: Professor Rob Knight of the University of Colorado Boulder, who collaborates with Spector, famously showed that transferring gut bacteria from obese humans to mice could make the rodents gain weight.

First of all – the paper they link to does include Rob Knight as a co-author, but the corresponding and senior author is Jeffrey Gordon and Rob is fourth to last (mind you I love Rob and his work, but in this case, saying this is something Rob showed without mentioning Gordon is just not right).

4 . The sentence with the reference to Rob Knight is just bad reporting #2

What the *$*$# does “famously showed” mean? Really.  What does it mean?

5 . The sentence with the reference to Rob Knight is just bad reporting #3

The statement “Previous studies made similar findings” is just so incredibly misleading.   It seems to be referring back to the previous sentences:

“What is emerging is that changes in our gut microbe community , or microbiome, are likely to be responsible for much of our obesity epidemic, and consequences like diabetes, cancer and heart disease,” he said. “It is clear that the more diverse your diet, the more diverse your microbes and the better your health at any age.”

This is just completely overblown.  The more diverse your diet the better your health at any age?  Oh #FFS that is just not based on any science.  And the “likely responsible for” is silly too.

6 . The sentence with the reference to Rob Knight is just bad reporting #4

Why exactly tell us he is collaborating with Rob Knight?  So some of Rob’s good work rubs off?  I mean, Spector may do some fine work (and he has done some really good stuff).  But casually mentioning he collaborates with Knight who famously showed something (when actually it was more Jeff Gordon’s work) which did not actually show what the article implies it showed.  Aaaaaaaaaaarg.

7. Good news.

Spector’s book claims that the diversity of microbes in the human body has decreased almost a third over the last century. But there’s also good news: Foods like dark chocolate, garlic, coffee and Belgian beer may help increase gut microbes.

Really?  Thinking about microbes MAY also increase gut microbes.  And so might listening to NPR.  Not something worth reporting here.

8. This sentence

This discovery suggested to his father that many cases of obesity may not simply be due to overeating.

That is right.  Looking at his son’s poop and the microbes in it is the key to knowing that obesity might actually be fuc$*@#@ complex and not only caused by overeating.  Oh, that and 100 years of epidemiology and research.

9. This sentence

“Once on the diet I rapidly lost 1,300 species of bacteria and my gut was dominated by a different group called bacteroidetes. The implication is that the McDonald’s diet killed 1,300 of my gut species,” he said.

Sorry but that is NOT the implication.

UPDATE 1: May 11, 2015. 8:00 PM

Thanks to a Tweet from Jennifer Gunter I changed the title of my post from ” 9 things horribly wrong with Newshour story on fast food and microbiomes” to “9 things PBS Newshour famously gets horrible wrong in story on fast food and microbiomes”

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——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Cell Symposia have a problem with gender balance of speakers

With apologies I don’t have time right now to tease apart all the details on these meetings. But, yuck. Cell Symposia have a big and persistent problem with gender balance of speakers. See the Storify below:

//storify.com/phylogenomics/cell-symposia-gender-balance-problems/embed?border=false&template=slideshow//storify.com/phylogenomics/cell-symposia-gender-balance-problems.js?border=false&template=slideshow[View the story “Cell Symposia Gender Balance Problems” on Storify]


——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Coming today to a cat near you – microbes

Only three years after first imagined … https://www.kickstarter.com/projects/catbiome/kittybiome-kitty-microbiomes-for-cat-health-and-bi/widget/video.html https://www.kickstarter.com/projects/catbiome/kittybiome-kitty-microbiomes-for-cat-health-and-bi/widget/card.html?v=2

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

FuturePhy, Call for Participation

Just got this via the email tubes:

FuturePhy is an NSF-sponsored, three-year program of conferences, workshops and hackathons on the Tree of Life. The project aims to promote novel, integrative data analyses and visualization, interdisciplinary syntheses of phylogenetic sciences, and cross-cutting uses of phylogenetics to develop and address new research questions and applications.

The first phase of this mission is critical: to bring together a broad community of people from diverse backgrounds who are active in phylogenetics research, who use the tree of life in research or education, who will benefit in applied or practical ways from a comprehensive tree of life, or who come from a background that offers new perspectives on defining, addressing or transcending key challenges in phylogenetics.

Help accelerate progress in all aspects of phylogenetics research by joining FuturePhy today. Diverse opportunities will be available to attend FuturePhy sessions in person or virtually, and to link FuturePhy to existing projects and initiatives.

We invite you to participate in the project in several ways:

1. Register on http://futurephy.org Scientists from all aspects of the phylogenetic sciences, educators, members of the tree-using community, and others interested in phylogenetics are welcome.

2. Contribute to the discussion forum on http://futurephy.org This is the best way to log your interest and contribute ideas.

3. See our main themes, comment on them and take the survey to rank them: https://www.surveymonkey.com/s/8CWXMRF

4. Email contact with ideas or comments

5. Tweet to the FuturePhy community: @FuturePhy

6. Comment in the FuturePhy thread on http://phylobabble.org

At #UCDavis 5/8 – Special seminar on bees and parasites

Special Seminar: Entomology, Bee biology

"Pesticides, parasites and pollinators: the impacts of environmental stressors on bees"

Prof Nigel Raine Univ of Guelph

Date: Friday May 8
Time: 1 PM
RM: 366 Briggs Hall