Eisen Lab Blog

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.
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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.

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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.

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
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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.

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6/10 at #UCDavis: Workshop on “The Social Life of Medical Data”

The Social Life of Medical Data

A one-day workshop on sharing, pooling and appropriating medical information

http://icis.ucdavis.edu/?tribe_events=workshop-the-social-life-of-medical-data

Wednesday, June 10, 10 am to 5 pm
UC Davis campus (location TBA)

Once digitized, medical information – such as data, images, standards, and codes – travels across different spaces and communities. Smartphones produce and transmit data coming from our bodies, which is shared and discussed in social media platforms and then gathered and analyzed in data centers. Medical information intended for professional use can be appropriated, circulated and used to create communities of caring or participate in biomedical research. At the same time new power asymmetries can emerge, as public institutions and private corporations claim control over increasingly valuable health data.

In this one-day workshop we will analyze the trajectories of digitized medical data. We will discuss how patient communities, care providers, social activists, governments and corporations are designing, fostering and managing alternative approaches to healing and increasingly look towards open source, distributed, and participatory research to do this. Data created from bodies has the potential to expand our understanding of health-related research and scholarly communication practices.

In addition, we will explore different ways of including patient communities in participatory design of tools that assist in the management and analysis of health data. We aim to foster a discussion amongst anthropologists, media scholars and biomedical researcher about the emergent forms of sociality and the politics of health and illness in our digital era.

Speakers include:

Nick Anderson, UC Davis
Carlos Andres Barragan, UC Davis
Dav Clark, UC Berkeley
Alessandro Delfanti, UC Davis
Joe Dumit, UC Davis
Allison Fish, UC Davis
Marina Levina, University of Memphis
Hélène Mialet, UC Berkeley
Kim Surkan, MIT
Orkan Telhan, University of Pennsylvania

Detailed program TBA

Lunch will be served. Please RSVP at this link if you plan to attend http://bit.ly/1PxzbQ6

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UC Davis Innovating Communication in Scholarship
icis.ucdavis.edu

Post-doctoral position in Human Microbiome Research and Women’s Health

POSTDOCTORAL POSITION BIOINFORMATICS & HUMAN MICROBIOME RESEARCH

The Institute for Genome Sciences at the University of Maryland School of Medicine encompasses an inter-disciplinary, multi-departmental team of collaborative investigators with a broad research program related to the genomics of infectious diseases, human microbial metagenomics, functional genomics, and bioinformatics.

TWO POSTDOCTORAL FELLOW positions are currently opened at the Institute for Genome Sciences for collaborative projects between Drs. Jacques Ravel and Rebecca Brotman. Qualified candidates will be enthusiastic, highly motivated and interested in studying the role of the human microbiome in relation to women’s health. The research in this position will focus on how the vaginal microbiome provides protection from sexually transmitted infections (STIs) and in the development of bacterial vaginosis (BV). Projects will apply computational, statistical and bioinformatics approaches on multi-omics’ datasets such as genome sequences, metabolomics, metagenomics, and metatranscriptomics.

The ideal applicant will possess a demonstrable understanding of bioinformatics and computational biology with a background in molecular biology, microbial ecology, statistics and/or molecular epidemiology. The candidate will have a doctoral degree in Genetics, Biology, Microbiology, Computer Science or a related field. Programming and statistical skills in languages such as Perl, Python, C/C++ and R, though not essential, are a plus.

Postdoctoral fellows at IGS benefit from a community of interactive research labs, bioinformatics experts and a variety of state of the art sequencing, and computational resources in a world-class institute dedicated to genomic, basic, and translational research.

To apply, please send a CV, a statement of research interests (2 pages maximum), and contact information for three references to IGS-jobs.

Additional inquiries about the position can be sent to Drs. Jacques Ravel and Rebecca Brotman

jravel@som.umaryland.edu
rbrotman@som.umaryland.edu

Ravel Brotman bioinformatics postdoc description.pdf

CPB Seminar at #UCDavis today: Environmental gradients and interactions with soil biota shape adaptation in teosinte

CPB Spring Quarter Seminar Reminder – Tuesday, May 19, 2015 – 4:10pm – 1022 Life Sciences

May 19: Anna O’Brien
Graduate Student, Population Biology Graduate Group, UC Davis
Title: “Environmental gradients and interactions with soil biota shape adaptation in teosinte”

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    

http://blogs.kqed.org/science/files/jw-player-plugin-for-wordpress/player/player.swf

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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.

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At #UCDavis today Sam Diaz-Munoz, 11:15 am

Department of Microbiology & Molecular Genetics Recruitment Seminar

Samuel Diaz-Munoz, Ph.D.
(NYU)

"The Evolution of Viral Social Interactions"

Monday, May 18, 2015

11:15 am*


197 Briggs*

*note time and location

Diaz-Munoz Seminar 5-18-15.doc

Talk at #UCDavis today: Michael Fischbach on Small molecules from the human microbiota – GBSF noon

Seminar today

“Insights from a global view of secondary metabolism: Small molecules from the human microbiota”

Michael Fischbach, Ph.D.

Assistant Professor, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco

Friday, May 15, 2015 12:10 – 1:00 PM

Genome and Biomedical Sciences Facility Auditorium (GBSF 1005)

Fischbach.pdf

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

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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.

——–