Overselling the mcirobiome award: Dr Roizen's Preventative and Integrative Medicine Conference

Just got an email announcement for "Dr. Roizen's Preventative and Integrative Medicine Conference" in Las Vegas in December 2015.

The announcement did not start of well for me with the gender balance of the key speakers

But since I spoke at this meeting in 2013 and since there was a good gender balance at that meeting, I decided to give the benefit of the doubt and keep reading (though I note - not trying to say this 5:0 gender ratio is a good thing).

And this is when it got worse - here are the bullet points for what one should learn from attending this meeting

• The key concept about optimal aging that Dr. Roizen learned from 56 million people who took the RealAge® test
• Smart tips about changing you and your patient's microbiomes and what to do for your microbiome to promote weight loss and how it inhibits aging
• How you can affect the role of the GI tract in chronic disease
• How to understand the clinical utility of TMAO testing for monitoring cardiometabolic risk
• The tricks about measuring your microbiome's effects
• Why some choose a plant based diet and why you might not
• What supplements do you and your patient's need with a plant based diet to decrease inflammation and improve your microbiome
• Clarify how a systems-based approach can effectively treat illness and promote wellness

Now - I don't know much about Dr. Roizen or his optimal aging claims in his books (I am skeptical). But the microbiome stuff in here is silly.

Let's start with: "Smart tips about changing you and your patient's microbiomes and what to do for your microbiome to promote weight loss and how it inhibits aging".  I wonder how he will give these smart tips when as far as I know there is nothing actually known about this.  How the microbiome inhibits aging?  Really? Is this going to be a summary of future research not yet done or even imagined?

What about "The tricks about measuring your microbiome's effects."  So - there are 1000s of scientists studying this, they mostly say it is very very very hard to study the effects of the microbiome and Roizen and crew are going to solve this with a few "tricks"?  So is he saying everyone in the field is incompetent since they can't measure these effects but he knows how to with a few tricks?

Dr. Roizen seems like a smart person and some of what I have heard from him sounds reasonable.  These microbiome claims from him here are a clear example of "Overselling the microbiome" and buying into the hype and not staying with the science. Maybe he was not paying attention for my talk for this meeting in 2013 when I discussed overselling the microbiome

I hope he tones down his claims in the future ... but for now he is a winner of a coveted "Overselling the Microbiome Award".  For other "winners" see here.

Blind trust in unblinded observation in Ecology, Evolution and Behavior (Guest Post by Melissa Kardish)

This is a guest post from Melissa Kardish - a PhD student at UC Davis - writing about a recent paper from work she did at her prior position.  The citation for the paper she is writing about is below:

Kardish MR, Mueller UG, Amador-Vargas S, Dietrich EI, Ma R, Barrett B and Fang C-C (2015) Blind trust in unblinded observation in Ecology, Evolution, and Behavior. Front. Ecol. Evol. 3:51. doi: 10.3389/fevo.2015.00051

Here is her post.

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Blind trust in unblinded observation in Ecology, Evolution and Behavior

We recently published our study in Frontiers in Ecology and Evolution where we found that a remarkable number of studies that could be affected by observer bias didn’t indicate whether or not they blinded their research. In fact only 13.3% of studies reported this:

We tried to make this a very transparent study. In addition to journal level data in the main article, we include in our supplemental material a table with the score for every article we read for this study (a summary of these scores per journal can be found in Figure S2 included here). If anything, our results under-represent the amount of studies that could have been scored blind (the real underreporting/underuse of blind observation is probably less than the 13.3% we report). For instance, we did not assess that there was potential for bias in the scoring of microsatellite markers (scored as unlikely to have observer bias). However, we did identify one study which was based on data from microsatellites which did blindly score their markers and report this scoring in their methods (and was therefore scored as “blind” in our study).  We also considered a study blind in its entirety for the purposes of our scoring if only one aspect is reported even if other experiments could also have been influenced by observer bias (Check out our supplemental methods for more ways we conservatively scored in our study).

We recognize that not all EEB studies can be blinded due to a variety of logistical or hypothesis driven reasons; however, we encourage such studies to accurately report this rationale and consider and attempt to minimize observer bias when designing experiments.

Thus far we have had a great response from the surveyed journals. Many of them have notified their editors about the lack of blind observation that we found reported in their journal. One journal has even notified us of plans already in place to address this issue at their next editorial board meeting.

We’re excited to have this work out there and hope this will inspire people to blind their studies and accurately report the science they are doing. We’re also excited to have the study published in an open-access format where we hope the encouragement for blind observation can reach all levels of science. Finally, as reporting of science in our fields improves in the coming years, we hope this study can serve as a template to address other potential concerns in experimental design and reporting.

For our article check out:  http://journal.frontiersin.org/article/10.3389/fevo.2015.00051/full

For our supplemental text and methods: http://journal.frontiersin.org/file/downloadfile/10238/octet-stream/Data%20Sheet%201.PDF/711/2/142945

For our data table with each of the articles we surveyed: http://journal.frontiersin.org/file/downloadfile/10235/octet-stream/Table%201.XLSX/711/1/142945

Nice story from Dan Potter on KQED about Women Science PhDs

Nice story on KQED from Dan Potter: Women Getting Science Ph.D.s Still Face Gender Barriers    

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:

Oxford Global’s Pharmaceutical IT Congress: All 38 speakers male! (it seems)
http://t.co/ctu18mKLAw
@phylogenomics @GenderAvenger #YAMMM

— Elisabeth Bik (@MicrobiomDigest) May 13, 2015

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

http://www.bmsystems.net/download/BioMarkers-BMsystems-conferenceprogramme.pdf

https://web.archive.org/web/20120514151415/http://www.ngsasia-congress.com/

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.

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

Fast food kills gut bacteria that can keep you slim, study finds http://t.co/3fPIhJTuAB | @newshour

— PBS (@PBS) May 11, 2015

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"

@PBS famously showed bad science reporting https://t.co/8VuGq5njWU

— Jennifer Gunter (@DrJenGunter) May 12, 2015

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: