NIH Announces Revised Genome Data Release Policies
Just got notified of this by the UC Davis Med. School grants administration: NOT-OD-14-124: NIH Genomic Data Sharing Policy. Lots of interesting things in here including a summary of the comments that they received on the draft policy.I have copied some of the more interesting and relevant bits below:Sharing research data supports the NIH mission and is essential to facilitate the translation of research results into knowledge, products, and procedures that improve human health. NIH has longstanding policies to make a broad range of research data, in addition to genomic data, publicly available in a timely...
Source: The Tree of Life - August 30, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
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 organi...
Source: The Tree of Life - August 30, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
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 scientis...
Source: The Tree of Life - August 30, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Kudos to Dr. Roizen's Personalized, Preventive, & Integrative Medicine "Focus on Women's Health" Conference #NoMoreYAMMMs
Quick post here as I have a bit of a cold. I post a lot of critiques here about meetings that have bad gender ratios for the speakers. But I do focus on the negative and am trying to also call attention to the good cases. Well here is one: the 12th Annual Dr. Roizen’s Personalized, Preventive, and Integrative Medicine Conference with a focus on Women's Health. And unlike the recent Ovarian Club meeting (see No Ovaries? Well this Ovarian Club Conference is For You (YAMMMs for everyone)) which had few female speakers despite the topic, Dr. Roizen and the other organizers (including one of ...
Source: The Tree of Life - August 29, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Overselling the Microbiome Award: The Microbiome Diet Book
Well, umm, I do not know what to say: The Microbiome Diet: The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss: Raphael Kellman MD: 9780738217659: Amazon.com: Books. I got pointed to this book by Dorothy Timmermans and she wondered if this was a case of "overselling the microbiome" or not. I guess I don't know because I have not read the book. Nor will I most likely. But I think almost certainly it is a case of "Overselling the Microbiome" based just on reading the blurb on Amazon from the Publisher which I paste below. It contains a litany of over t...
Source: The Tree of Life - August 26, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
The Agricultural Bioscience International Conference #ABIC2014 run by @ABICFoundation: where you can hear lots of talks by men #YAMMM
Well, here is this week's YAMMM (yet another mostly male meeting) alert: The Agricultural Bioscience International Conference in Saskatchewan.Male Speakers: 40Female speakers 4Marc AlbertsenRobert CarberryDavid FischhoffMaurice MoloneyFrédéric SeppeyJuliana AlexandreTom CarratoMichael FrodymaCarlo MontemagnoTim SharbelSimon BarberDavid ChalackRichard GrayGiuseppe NataleRoman SzumskiRoger BeachyRaju DatlaWayne HunterMatthew O'MaraAlbert VandenbergSuzanne BertrandSwapan DattaDavid IrvinPeter PhillipsVictor VillalobosJulie BorlaugMaurice DelageLawrence KentIngo PotrykusSimon WarnerJim BrandleDavid DentGanesh KishoreAnd...
Source: The Tree of Life - August 25, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Want to prevent someone from taking copyright on something- have it be made by a monkey
Well, this is both strange and surreal and fascinating: Who Owns A Monkey's Selfie? No One Can, U.S. Says : The Two-Way : NPR. Turns out the UC Copyright office says a photo taken by a monkey cannot by copyrighted because apparently copyright is reserved for humans (and I guess human corporations). NPR implies that an Ars Technica article by David Kravets is what caught their attention as well as that of others.I wonder - if one could teach a monkey to type maybe one could get them to type up some papers and then nobody could have copyright on them? What if one wrote a paper where a monkey was a...
Source: The Tree of Life - August 22, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
No Ovaries? Well this Ovarian Club Conference is For You (YAMMMs for everyone)
Well, I just got an email invitation to attend CME - OVARIAN CLUB 4. And alas, rather than just dumping it into SPAM (which I did do) I clicked on one of the links. I had to know - what was the gender balance at this meeting. Was there any chance that the organizers would see that it would be ironic to not have a decent number of female speakers? Alas, nope.The organizing committee is 17:1 males to females.And the speaker balance is not much better something like 25:6.I guess maybe they should rename this "Meeting brought to you by people who mostly do not have ovaries." Sad. Anothe...
Source: The Tree of Life - August 21, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Nice Art and Science example - UC Davis Medical School molecule sculpture
Quikc post here. A month or so ago I went to the UC Davis Medical School in Sacramento for a meeting and got to see this amazing new sculpture for the first time.For more about this and the Artist Roger Berry see this article. It is always inspiring and uplifting to see nice architecture and nice art in a science building.
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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.
-------- (Source: The Tree of Life)
Source: The Tree of Life - August 20, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Today's YAMMM (Yet another mostly male meeting): pharma-nutrition #PN2015
Just got pointed to (by Elisabeth Bik) an announcement for a meeting: Home : Pharma-Nutrition 2015 with a focus on "Linking the Microbiome with Nutrition and Pharma". And alas, the list of confirmed speakers is as follows:Keynote SpeakerMartin J. Blaser, NY University Medical Center, New York, NY, USASpeakersGregor Reid, University of Western Ontario, London, ON, Canada Alain van Gool, Radboud University, Nijmegen, The Netherlands David Hafler, Yale, New Haven, CT, USA John F. Cryan, University College Cork, Cork, Ireland André Marette, Laval University, Montreal, QC, Canada Charle...
Source: The Tree of Life - August 20, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
No #AAAS and ASM you do not deserve good PR for freeing up a few papers on Ebola
Saw a PR from AAAS about how they were freeing up all of ~ 20 papers on Ebola In light of what has become the largest Ebola outbreak on record, Science and Science Translational Medicine have compiled over a decade's worth of their published news and research. Researchers and the general public can now view this special collection for free.OK. More access is good. But alas, they did not even free up all papers in #AAAS journals with Ebola in the Title or Abstract.And then I started thinking. What about HIV? TB? Malaria? And as I started Tweeting about this, I saw that ASM also was hopping on the "free Ebola" bandwago...
Source: The Tree of Life - August 20, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
AAAS - Blocking Access to the Scientific Literature Even When They Say It Is "Free"
Today, I wanted to show someone a PDF of a paper of mine that I co-authored in 1999. The paper was, I think, kind of cool. It reported the sequencing and analysis of the genome of Deinococcus radiodurans, an incredibly radiation resistant bacterium. Alas, I did not have a copy on me, and the only electornic device I had with me was my phone. The person I wanted to show the paper to had their computer, a device with a strange little red trackball and running some sort of Windows operating system, so I looked at it and panicked and said "Maybe you should drive" (as in, maybe they should be the one con...
Source: The Tree of Life - August 18, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Today's YAMMM (Yet Another Mostly Male Meeting) Brought to You by CIFAR & NAS
Well, just got an invite to this meeting: Symbioses becoming permanent: The origins and evolutionary trajectories of organelles. The topic seems of direct interest to what I work on. And, it is relatively close (Irvine is a short hop away). So this could be a way to go to a meeting without having to travel too far. And maybe I could see my younger brother Matt who lives in LA and just graduated from UC Irvine's Masters program in Sound Engineering. Then I looked at the schedule of speakers and organizers. Many are friends. Many others are colleagues. Could be fun to see some p...
Source: The Tree of Life - August 15, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
AAAS and SnapChat collaborate to develop SnapScience to publish scientific papers transiently
Just got this in an email and thought it should be shared.Washington, DC. August 15, 2014.Kent Anderson, the newly appointed Publisher of AAAS (see http://www.aaas.org/news/aaas-names-new-science-publisher) has announced his first action as Publisher - a partnership between AAAS and Snapchat (https://www.snapchat.com).Anderson said "Although I will not officially assume the role of Science publisher until 3 November, this was too important a task to not carry out immediately. AAAS has always been looking for new ways to reduce the public availability of scientific publications. AAAS approached Snapchat a few months ago an...
Source: The Tree of Life - August 15, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
An important read: Emma Pierson on gender and authorship position in science
This is a fascinating read: In Science, It Matters That Women Come Last | FiveThirtyEight. By Emma Pierson, who works at 23 and me. It has all sorts of references of use and details on authorship position in scientific publications and how gender and author position are correlated. Definitely worth a read.
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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.
-------- (Source: The Tree of Life)
Source: The Tree of Life - August 14, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
