Wednesday, February 25, 2015

Today's all male genomics meeting brought to you by Oxford Nanopores

The Tweets about this really say it all so I am just going to embed them here:









Really disappointed in Oxford Nanopores.  Perhaps we can get some of the speakers to cancel on them unless they fix things.
  • Ron Ammar, University of Toronto, Canada
  • Ewan Birney, European Bioinformatics Institute, UK
  • Thomas Hoenen, NIH/NIAID, USA
  • Nick Loman, University of Birmingham, UK
  • Brook Milligan, New Mexico State University, USA
  • Justin O’Grady, University of East Anglia, UK
  • Jared Simpson, Ontario Institute for Cancer Research, Canada
  • Yutaka Suzuki, University of Tokyo, Japan
  • Mick Watson, The Roslin Institute, University of Edinburgh, UK
Update 3/8/15 

Well, after I posted about the Nanopore meeting there were some responses on Twitter. So I made a Storify

So I decided to check the meeting today to see whether they "fixed" anything.

Right now they list 11 male and two female speakers.  So that added two males and two females.  Better ratio.  Still pretty bad.  They really could do better ...



Thursday, February 19, 2015

Oxford Global Sequencing Meetings: Where MEN Tell You About Sequencing #YAMMM

Well, got an email invite to one of these Oxford Global Meetings. Sadly the gender ratio of listed speakers is awful. I highlighted the list below (men in yellow, women in green).  Ratio of 17:3.  (See below).  No thanks Oxford Global.

Dear Professor Jonathan Eisen ,
 We hope you are well and we would like to invite you to speak at our forthcoming Next Generation Sequencing (NGS) USA congress (www.nextgenerationsequencingusa-congress.com) or co-located  Single Cell Analysis USA congress (www.singlecellusa-congress.comto be held on 27th -28th October 2015 at Harvard Medical School, Boston, USA.
 Over the two days, the NGS USA congress aims to cover updates and application of NGS technologies in genomics and genetics research in the US and UK, Europe. Topics are comprised of NGS & NGS Data Analysis Technologies and Platforms, NGS for Cancer Drug Development, Microbiology and Immunotherapy as well as Clinical Applications & Diagnostics. Novel updates in Gene Synthesis, Protein Sequencing and Targeted Sequencing will also be explored The Single Cell Analysis USA congress looks at new methods in DNA sequencing, epigenomic DNA sequencing and RNA sequencing, informatics, data handling as well as application of single cell genomics in understanding cancer  other areas of cancer research such as cancer stem cells and immunotherapy. The presentations are also comprised of novel techniques in imaging and cytometry, isolation and processing of single cells. The congress also covers the applications in translational medicine and the clinic for therapeutic targeting.
 The combination of carefully researched topics and high-level networking opportunities creates a unique discussion platform for over 250 senior scientists we are expecting in attendance from research institutions and pharmaceutical companies. Confirmed Speakers for 2015 include:NGS·          Sreekumar Kodangattil, Senior Principal Scientist, Pfizer       
·          Shrikant M. Mane, Senior Research Scientist in Genetics; Director, MBB Keck Biotech laboratory; Director, Yale Center for Genome Analysis
·          Stephan Schuster, Professor of Biochemistry and Molecular Biology, Penn State University
·          Richard  McCombie, Professor, Human Genetics, Cold Spring Harbor Laboratory
·          Jingyue  Ju, Director, Center for Genome Technology and Biomolecular Engineering, Professor of Chemical Engineering and Pharmacology, Columbia University            
·          Christopher Mason, Chair, ABRF NGS Consortium, Assistant Professor, Weill Cornell Medical College. Dept. of Physiology & Biophysics; The Brain & Mind Research Institute
·          Michaela Bowden, Associate Director, Center for Molecular Oncologic Pathology, Dana Farber Cancer Institute      
·          Yuan Gao, Director, Associate Professor, Lieber Institute/Johns Hopkins University
·          Sheng Li, Instructor in Bioinformatics, Department of Neurological Surgery, Weill Cornell Medical College
·          Michael  Fraser, Associate Director, CPC-GENE Prostate Cancer Genomics Program, Princess Margaret Cancer Centre    
 Single Cell·          Daniel Chiu, Professor, University of Washington    
·          Steve Potter, Professor, Division of Developmental Biology, Cincinnati Children's Medical Center
·          Norman Dovichi, Professor, University Notre Dame 
·          Zaida Luthey-Schulten, Professor of Chemistry, University of Illinois
·          Paul Bohn, Professor of Chemical and Biomolecular Engineering, University of Notre Dame       
·          Navin Varadarajan, Assistant Professor, University of Houston
·          Alexander R., Ivanov, Director of the HSPH Proteomics Resource, Research Scientist
Harvard School of Public Health·          Viktor Adalsteinsson, Researcher, Researcher, Koch Institute at MIT, Broad Institute of MIT and Harvard Medical School
·          Xinghua Victor Pan, Research Scientist, Single Cell Genomics Group, Sherman Weissman Laboratory, Department of Genetics, Yale University School of Medicine
·          Cheng-Zhong Zhang, Computational Biologist, Department of Medical Oncology, Dana-Farber Cancer Institute




Tuesday, February 17, 2015

Two Eisen lab papers selected for the PeerJ 2015 Collection

Cool.  Two paper from my lab were selected as highlights of 2014 papers in the Peer J: PeerJ Collection: PeerJ Picks 2015 Collection

The papers were


,  ,  

Sunday, February 15, 2015

Overselling the microbiome award: CBC Fresh Air & JA Tetro on kissing microbiomes

Well, so there I was, enjoying a relatively peaceful and quiet Valnetine's day.  When I noticed a Tweet directed to me from one of my favorite scientist's out there
So I decided to check it out.  I clicked on the link and got to a CBC Fresh Air news story on Soundcloud:

▶ Kissing and romance and bacteria with Jason Tetro Feb 14/15 by CBC Fresh Air

I plugged in my headphones (was not sure if my kids should hear it) and listened away.  And what I heard was excrutiatingly painful.  The CBC Fresh Air reporter was discussing kissing and the microbiome with JA Tetro.  And Tetro made some of the most misleading, ridiculous overstatements about the microbiome I have heard in many years:
  • He basically implied or specifically said that, in humans, attraction to partners and relationship success was determined by finding a partner with similar microbiomes to oneself.  
  • Furthermore he discussed how maintaining similar microbiomes (e.g., via consuming the same probiotics or fermented foods) would help maintain attraction and how things like travel away from a partner might lead to repulsion.  
  • He said things like tha our immune systems determine if a partner is right for you from kiss-based comparison of a partner's microbiome to one's own.  
  • And that if the microbiome in a kissing partner is a match this leads to bliss and addiction and that salive is the first line of defense when it comes to relationships.  
  • He even went so far as to say that this is all about "trying to find your mother because our microbiomes come from our mother."  
I could do on and on.  It was the worst, most misleading, innacurate material I have probably ever heard about microbiomes.  Tetro and CBC Fresh Air should be ashamed.

Sadly, I found some other misleading, inaccurate material from Tetro about the same topic in an article about kissing microbiomes from a few months ago: Swapping spit and testing chemistry: How kissing, germs help you pick your partner where Tetro is quoted
Tetro says that when you kiss your date, his or her germs make their way into your mouth’s ecosystem. And if it’s a match, you’ll want to keep smooching. 
“This study does one amazing thing, it shows you that kissing is the best way to find a mate for the long term. It might sound really gross but if the bacteria from the other person harmonizes with your bacteria, your immune system is all good. You feel a sense of calm and happiness, maybe even addiction,” he explained. 
“But if the bacteria don’t align with your microbes, you actually feel disgust and revolt. Your immune system is rejecting that person as a possible mate.”
and
“This study proves that when it comes to finding the right mate, the old game of spin the bottle actually has a base in science,” he said. 
More completely inaccurate, made up material with no basis in science.  As far as I can tell, this is basically made up.  Sure there may be a theory behind this.  But to present it as established facts about the microbiome is ridiculous.

This is all a shame really since the paper which the CBC Fresh Air story is referring to is actually a perfectly fine paper and the authors of the paper do not seem to be pushing these over the top ridiculous ideas.  And for this terrible story I am giving CBC Fresh Air and JA Tetro an "Overselling the microbiome award".

Thursday, February 12, 2015

Twisted tree of life award: throwback PR from an ingrained Oregon State

Just got pointed to this PR:  Unwanted impact of antibiotics broader, more complex than previously known -- ScienceDaily

It has one of the worst microbe-evolution sections of text I have seen in a long long time:
Mitochondria plays a major role in cell signaling, growth and energy production, and for good health they need to function properly. 
But the relationship of antibiotics to mitochondria may go back a long way. In evolution, mitochondria descended from bacteria, which were some of the earliest life forms, and different bacteria competed with each other for survival. That an antibiotic would still selectively attack the portion of a cell that most closely resembles bacteria may be a throwback to that ingrained sense of competition and the very evolution of life.
Yup.  That antibiotics that target bacteria also affect mitochondria is a throwback to that ingrained sense of competition and the very evolution of life. 

Can anyone - anyone - please - please - tell me what that means?

For this, I am giving the folks from Oregon State a coveted Twisted Tree of Life Award.

Monday, February 09, 2015

Another "Yet another mostly male meeting (YAMMM)" from BGI

Well just saw an announcement for this meeting on Twitter: The First Announcement of The Tenth Annual Meeting of the International Conference on Genomics (ICG

And I hoped beyond hope that they would have a decent representation of women speakers at the meeting.  Why did I hope this?  Well, in the past, BGI run meetings have had incredibly skewed gender ratios of speakers.  See this post for a discussion of their past record: Kudos to the DOE-JGI for organizing a genomics meeting w/ a good gender ratio - no kudos to BGI - yet again

I guess I had hoped that perhaps they would try to change their practices after I and other people criticized them for their past record.  So - I went to the web site for the ICG10 meeting advertised in the Tweet.  Oh well, silly me for hoping.

On the front page they have 14 speakers they are promoting - all of them male.

Screen shot from ICG10 web site

On the announcement page they have a slightly different list where the ratio is 14:1
  • Jef Boeke, NYU Langone University School of Medicine, USA
  • Sydney Brenner, 2002 Nobel Laureate in Physiology or Medicine, Singapore
  • Charles Cantor, Sequenom, Inc., USA
  • Julio Celis, Danish Cancer Society Research Center, Denmark
  • Richard Durbin, Wellcome Trust Sanger Institute, UK
  • Leroy Hood, Institute for Systems Biology, USA
  • Thomas Hudson, Ontario Institute for Cancer Research, Canada
  • Maria Leptin, Chair of EMBO, Germany
  • Maynard Olson, University of Washington, USA
  • Aristides Patrinos, J. Craig Venter Institute, USA
  • Mu-ming Poo, University of California, Berkeley, USA
  • Richard Roberts, New England Biolabs, 1993 Nobel Laureate in Physiology or Medicine, USA
  • Eils Roland, Heidelberg University, Germany
  • Mathias Uhlen, Royal Institute of Technology, Sweden
  • Tilhuan Yilma, University of California, Davis, USA
Regardless, this is a consistent pattern of not having an even remotely balanced ratio of male to female speakers at their meetings.  And please, avoid their meetings until they change this.

Monday, February 02, 2015

Science based decision making in education: sleep and school start times in #DavisCA and beyond

In September of last year I wrote a brief post about science and decision making in schools: Nice letter to the editor in the Davis Enterprise taking on school district's anti-science tone.  I include it below since it is very relevant to this post.

----------------------------------
I assume many people heard about the recently released report from the American Academy of Pediatrics where they recommended high school classes start later in the morning than most do right now.  See for example: Let Them Sleep: AAP Recommends Delaying Start Times of Middle and High Schools to Combat Teen Sleep Deprivation.  And this report was covered in all sorts of newsy and bloggy places.   See for example, Amy Graff's article in SFGate and Deborah Netburn in the LA Times.  Overall, the argument presented by the AAP makes sense and seems supported by scientific fundings.  And they go through a lot of scientific reasons for their recommendations.

Alas, Winfred Roberson, superintendant of the Davis, CA schools (also known as the DJUSD) told the Davis Enterprise that the schools here would not be making any changes in response to this report:

“While DJUSD won’t be modifying start times, our role as an educational institution can be to find ways to support our students by giving them the tools that will help them to think through, make adjustments and prioritize their competing forces that may be cutting into the recommended sleep time,” Roberson said. “These are life skills we are helping to build that will help students to function even after graduation.”
And I had missed out on this quote, thankfully, but became aware of it when my wife showed me this letter by Steve Carlip in the Davis Enterprise today:  Don’t ignore the science Davis Enterprise.   I quote from it below:
The superintendent’s response, as reported in Tuesday’s Enterprise, was to simply ignore the science. Instead, he said, the schools will help student “build life skills” to “prioritize their competing forces that may be cutting into the recommended sleep time.” 
Really? The high school is going to teach students to control their circadian rhythms? It’s going to give them the “life skills” to regulate the timing of their bodies’ secretion of melatonin? It will educate them to overcome biological sleep-wake phase delay by sheer force of will?
He completely nailed it here.  I hope Winfred Roberson and the Davis School district rethink their attitude towards scientific studies.
-----------------------------------

Today I found out that the Davis School Board may actually be listening to the science.  For the next school board meeting which is February 5 there is an agenda item on this topic c. Update on the Formation of a DJUSD Sleep Study Committee. The description of the agenda item is as follows:
In August 2014, the American Academy of Pediatrics released a scientific sleep study report that recommended an 8:30 am start time for schools, which would allow secondary students more time to sleep.  The report generated community discussions and concerns since Davis secondary schools start before 8:30 am.
In response, the superintendent initiated the formation of a Sleep Study Committee (made up of students, teachers, counselors, parent/community members and administrators) to examine the benefits and logistical challenges of an earlier school start.    
This update is a report of the formation of the Sleep Study Committee and their charge.  For reiteration, at this time, staff is not offering recommendations about a modified start time.  Staff will wait to review the work of the Sleep Study Committee before offering formal recommendations to the Board. 
So I started digging around for more on the topic and found some things worth reading  But the most interesting thing I found was that there has been a discussion about this exact issue in the county where I grew up: Montgomery County Maryland.  Some of the articles about this area listed below:

It seems to me that Davis, CA really needs to consider this as a possibility.  It could help students in many ways and seems to be a relatively easy (though not free of course) way to improve the lives and learning of students in our town.  I am thrilled that the Board is bringing the topic up again.  Any examples out there of places that have shifted start times based on the AAP recommendation would be great (and what happened ...). 

See some responses on Twitter:



Best post doc position ever: w/ Jessica Green, myself, Jay Stachowicz, Jenna Lang

copied from U. Oregon web site

Postdoctoral Research Scholar
Institute of Ecology and Evolution

Posting: 14431
Location: Eugene
Closes: Open Until Filled

Revised Posting
Postdoctoral Position in Microbial Ecology and Evolution
Jessica Green at the University of Oregon (http://pages.uoregon.edu/green/) is currently seeking a postdoctoral researcher to collaborate on the Seagrass Microbiome Project (http://seagrassmicrobiome.org).  

Applicants should have a Ph.D. in a biological, computational, mathematical, or statistical field and strong writing skills.  The ideal candidate will have experience developing and applying models to understand the ecology, evolution, and/or function of complex systems.  Experience in the analysis of environmental sequence data is highly desirable, but not required. 
  
The successful candidate will have the opportunity to creatively and independently tackle one or more of the science questions outlined in the Seagrass Microbiome Project grant proposal (http://seagrassmicrobiome.org/2014-grant-proposal/), funded by the Gordon and Betty Moore Foundation.  

The successful candidate will interact regularly with team members Jonathan Eisen (http://phylogenomics.wordpress.com), Jay Stachowicz http://www-eve.ucdavis.edu/stachowicz/stachowicz.shtml, and Jenna Lang (http://jennomics.com/) at the University of California, Davis through weekly tele-conferencing and also through regular visits to the UC Davis campus. 

At the University of Oregon, the candidate will benefit from ongoing microbiome research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology (http://meta.uoregon.edu/) and the Biology and Built Environment Center (http://biobe.uoregon.edu/).

The position is available for 1 year with the possibility for renewal depending on performance.  The start date is flexible.  Please email questions regarding the position to Jessica Green (jlgreen@uoregon.edu).

To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references 
Submit materials to ie2jobs@uoregon.edu.  Subject: Posting 14431

To ensure consideration, please submit applications by March 10, 2015, but the position will remain open until filled. Women and minorities encouraged to apply.  We invite applications from qualified candidates who share our commitment to diversity. The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.

Storify of Day 1 of "An open digital global south meeting" at #UCDavis

I made a Storify of Tweets and some pictures from the "An open digital Global South" meeting that I am a co-organizer of. This was...