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




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: