Eisen Lab Blog

Nice letter to the editor in the Davis Enterprise taking on school district’s anti-science tone

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.

Funding and Ship-time Opportunities (XPrize, JAMSTEC and Simons)

Just got this email announcement from the Gordon and Betty Moore Foundation and thought the announcements would be of interest.

Dear colleague,

Here are some opportunities that have crossed our radar. We apologize for the spam.

XPrize’s latest innovation competition: Protect ocean pH
Summary: The organization behind Google’s $30 million sponsorship of a Lunar landing effort announced the roster of teams competing for the $2 million Wendy Schmidt Ocean Health XPrize focused on staving off ocean acidification.

Call for Pre-proposals: International Workshop for Large-scale Research Cruises Summary: In order to efficiently achieve the highest possible fulfillment of the research goals of its third medium-term research plans, the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) is planning long-distance, long-term multidisciplinary research cruises (large-scale research cruises) using its vessels that will be open to both Japanese and overseas universities and research institutes.

Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards Launched
Summary: The awards are intended to help launch and support the careers of outstanding young investigators who use quantitative approaches to advance our understanding of marine microbial ecology and evolution. Supported projects will focus on marine microbes or fundamental problems that are highly relevant to understanding marine microbial ecosystems.

Marine Microbiology Initiative

GORDON AND BETTY MOORE FOUNDATION
1661 Page Mill Road
Palo Alto, CA 94304

http://www.moore.org

Census of Deep Life call for proposals for sequencing metagenomes or 16S rDNA amplicons of communities from the deep subsurface.

Deep Carbon Observatory: Deep Life Community (DLC) Calls for Proposals

The DLC will accept electronic submissions until September 20, 2014 for proposals to the Census of Deep Life to support high throughput sequencing of metagenomes or 16S rDNA amplicons of communities from the deep subsurface. For more information, go to: https://deepcarbon.net/feature/call-proposals-census-deep-life-sequencing-deadline-20-september-2014#.VAZOZ0u5dFw

UC Riverside hiring a faculty member in Evolutionary Genomics

Letter Community Ecology-Biology to send.pdf
Evolutionary_Genomics_ad_v1.pdf

Session on microbial interactions at ASLO 2015 in Spain

Just got a conference announcement that seems of interest:

We would like to invite you to participate in our session “MICROBIAL INTERACTIONS ACROSS THE DOMAINS OF LIFE” (# 058) at the ASLO Aquatic Sciences Meeting in Granada, Spain, 22-27 February 2015. We welcome contributions on diverse types of microbial interactions, as well as evolutionary studies related to understanding microbial ecology. Please find more details in the flyer attached.
Feel free to pass this on to other colleagues who might be interested.

Deadline for Abstract Submissions: October 6, 2014
http://sgmeet.com/aslo/granada2015/
Session058_AquaticSciencesMeeting_Granada_Spain_Feb2015.pdf

The US Postal Service Cares (actually this was kind of a nice gesture)

Well, this is a new one for me and my family.  We got some mail today.  My wife called me over this evening to tell me and said “it might make something good for my blog”.  But it was very strange. From the US Postal Service.  In a plastic bag and the bag read “We care …” see below:

And inside of this was half of a piece of mail.  A card.  It felt very weird.  Like someone was censoring us but most likely some machine just ate the other half.

Front
Back

Add caption
They easily could have just tossed this once it got damaged.  Glad they did this.  Now, mind you, I still detest all their junk mail / bulk mail policies, but this was nice ..

9/10 AT #UCDAVIS – Brad Sherman on “Geographical Indications on Origin and Indigenous Knowledge”

sherman_09-10-14.pdf

Science Journal SPAM of the Week: the Journal of HIV/AIDS from Sci Forschen

Well, got this email this AM.  It is yet another spammy journal (I don’t work on HIV/AIDS).  I particularly like the part where I am called an “eminent personality”.

Dear Dr. Jonathan Eisen,
Greetings from the Journal of HIV/AIDS,
We take great delight in inviting you to join the Editorial Board for the Journal of HIV/AIDS , which is an open access, peer reviewed journal managed by Sci Forschen.  Ensuring quality and accuracy for every submitted article is the top most priority for Sci Forschen, and we genuinely believe that someone with the knowledge and experience, such as yourself, can really make a huge difference for us.
Journal of HIV/AIDS , publishes cutting edge research work submitted by scholars from all over the world, and we believe that your presence will polished up with the help of illustrious experts in research field.
We are always striving to involve eminent personalities like you and your standing in the global community makes us confident.
Kindly let us know your valuable response and acceptance if possible with in 48 hours.
Please kindly submit your following particulars to update in our journal website

1. Updated CV
2. Passport Size Photo
3. Short Biography
4. Research Interest

Looking forward for your valuable and soon response.
Regards,

Editorial Office
Sci Forschen Incorporation
913 Catkin Ct.
San Jose, CA 95128, USA.

A tale of salt and gender: participation of women in halophile research

Interesting paper on women in science of direct relevance to my work: Frontiers | Salty sisters: The women of halophiles | Extreme Microbiology.  I have been working on halophilic archaea for many years (since introduced to them in graduate school) and published papers on this topic (e.g., see The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon and Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux and more coming).  However, I have never been to a meeting dedicated to the topic and confess I have not thought specifically about the gender of scientists in this field and at meetings in the field and such.  Thus I was pleasantly surprised to see this analysis from Bonnie Baxter, Nina Gunde-Cimerman and Ahoren Oren.  Their abstract is below:

A history of halophile research reveals the commitment of scientists to uncovering the secrets of the limits of life, in particular life in high salt concentration and under extreme osmotic pressure. During the last 40 years, halophile scientists have indeed made important contributions to extremophile research, and prior international halophiles congresses have documented both the historical and the current work. During this period of salty discoveries, female scientists, in general, have grown in number worldwide. But those who worked in the field when there were small numbers of women sometimes saw their important contributions overshadowed by their male counterparts. Recent studies suggest that modern female scientists experience gender bias in matters such as conference invitations and even representation among full professors. In the field of halophilic microbiology, what is the impact of gender bias? How has the participation of women changed over time? What do women uniquely contribute to this field? What are factors that impact current female scientists to a greater degree? This essay emphasizes the “her story” (not “history”) of halophile discovery.

As part of their paper they analyze participation of women at conference on halophiles:

This is a useful analysis and compendium and it would be great to see this done for as many fields as possible. 

Mesquite "A modular system for evolutionary analysis" v3.0 released from Team Maddison

Just found out about this on Facebook via Rod Page: Mesquite V3.0  has been released.  Mesquite is from Team Maddison (Wayne and David).  I have been using their software since 1987 when I took Stephen Jay Gould’s course at Harvard and they were TAs for the course demoing an early version of MacClade.   Lots of nice features and it is available in Mac, Unix/Linux, and Windows versions.   They describe “What Mesquite Does” on their Wikispaces site in the following way:

Mesquite is software for evolutionary biology, designed to help biologists manage and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses and management features available depend on the modules installed. Here is a brief overview of some of Mesquite’s features. See also a more complete outline of features, and the Mesquite Project Youtube channel, with instructional videos helping you learn Mesquite.

Despite Mesquite’s broad analytical capabilities, the developers of Mesquite find that we use Mesquite most often to provide a workflow of data editing, management, and processing. We will therefore begin there.

Definitely worth a look.