Quick post – very interesting interview of Peter Suber by Richard Poynder

For those interested in Academic Publishing and OpenAccess issues this is really worth a read: Open and Shut?: Peter Suber on the state of Open Access: Where are we, what still needs to be done?.  It is an interview of Peter Suber by Richard Poynder.

UPDATE 10 minutes later – not saying I endorse or support everything Suber says (I am much more enthusiastic about gold open access than green OA which I find limited in use).  But the interview is worth a read.

Expansion of Academic Freedom at the University of California

Just got pointed to this revision of the UC Faculty Code of Conduct which was recently approved by the UC Regents: http://regents.universityofcalifornia.edu/aar/jule.pdf

I was pointed to it by Greg Pasternack from UC Davis who has been a major force in trying to guarantee academic freedoms at UC Davis.

Colleagues, 

  Four years and one month after the UCD Committee on Academic Freedom and Responsibility first raise the alarm about the danger of unjust discipline faculty in the UC system may face (and certainty have faced) for speech and actions regarding institutional matters, I am very happy to report to you all that on July 18 the UC Regents approved our proposed amendment to APM-015 that guarantees faculty academic freedom to speak out about institutional matters.  Given the number of judges that have ruled that faculty speech on institutional matters is *not* protected by the First Amendment, even in public universities, getting this freedom inscribed into APM-015 provides a policy-based guarantee no longer reliant on external interpretation. 

  See attached, notably the underlines in attachment 2.  You can also download it from http://regents.universityofcalifornia.edu/aar/aar.html under “committee on educational policy” 

  This is the greatest expansion in academic freedom in the history of the UC system, because all previous notions of academic freedom limited the application of the idea to just one’s area of scholarship.  Prior to this, the biggest change was to no longer require “dispassionate” scholarship.  However, academic freedom is no longer shackled to scholarship.  We are free to speak on all institutional matters, whether they are within our sphere of scholarship or not.  We may do so using any forum or medium. 

  Now go out and use your freedom to stir up brilliant controversies 😉 

Best wishes, 

-Prof. Greg Pasternack

The section he called particular attention to is in line 4 in the part on “Professional Rights of Faculty” which reads “freedom to address any matter of institutional policy or action when acting as a member of the faculty whether or not as a member of an agency of institutional governance.” This clearly relates to some real and perceived challenges to academic freedom at various UCs and it is good to have a formal policy that says such a freedom is a right of the faculty.

You go Greg …

Related posts:

A letter from Chair of the Board of Regents Bruce Varner

Forwarding this

Storify-based notes on #SMBE13 session on evolution of microbes and their genomes

Just finally getting notes up from the SMBE 2013 meeting session on “Diversity and evolution of microbes and their genomes” that I chaired.  After some issues with Storify I managed to record a “storification” with Twitter posts from the session. It is embedded below.

The talks were as follows:
Invited Talks

  • Holly Bik, UC Davis, Microbial Metazoa and the Taxonomic Abyss 
  • Lauras Katz, Smith College, Genome Dynamics across the Eukaryotic Tree of Life 
  • Jennifer Gardy, Of Snow and Short Reads: How Microbial Genomics Is Changing Public Health, British Columbia Center for Disease Control 
  • Tanja Woyke, Insights into the Phylogeny and Coding Potential of Microbial Dark Matter DOE Joint Genome Institute 

Talks selected from submitted abstracts

  • Pedro H. Oliveira: A Comparative Genomics Approach Provides New Insights into the Distribution and Evolutionary History of Restriction Modification Systems in Bacteria, Institut Pasteur 
  • Daniel J. Wilson, Genomic Insights into Within-Host Evolution and Pathogenesis in Staphylococcus aureus, University of Oxford 
  • John P. McCutcheon, Extensive Horizontal Gene Transfer Complements Missing Symbiont Genes in Mealybugs, U. Montana, 
  • Florent Lassalle, Biased Gene Conversion Shapes the Bacterial Genome Landscape, University of Lyon

New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria

(Cross post from my lab blog)

Quick post here.  This paper came out a few months ago but it was not freely available so I did not write about it (it is in PNAS but was not published with the PNAS Open Option — not my choice – lead author did not choose that option and I was not really in the loop when that choice was made).

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. [Proc Natl Acad Sci U S A. 2013] – PubMed – NCBI.
Anyway – it is now in Pubmed Central and at least freely available so I felt OK posting about it now.  It is in a way a follow up to the “A phylogeny driven genomic encyclopedia of bacteria and archaea” paper (AKA GEBA) from 2009 with this paper a zooming in on the cyanobacteria.

New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria

Quick post here.  This paper came out a few months ago but it was not freely available so I did not write about it (it is in PNAS but was not published with the PNAS Open Option — not my choice – lead author did not choose that option and I was not really in the loop when that choice was made).

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. [Proc Natl Acad Sci U S A. 2013] – PubMed – NCBI.

Anyway – it is now in Pubmed Central and at least freely available so I felt OK posting about it now.  It is in a way a follow up to the “A phylogeny driven genomic encyclopedia of bacteria and archaea” paper (AKA GEBA) from 2009 with this paper a zooming in on the cyanobacteria.

 

#PLOS Hub for Biodiversity – soon to be retired

Just got the email below.

Dear Subscriber,

We are writing to you as someone who is a registered user on PLOS Hubs: Biodiversity to let you know that we will shortly be retiring it.

Thousands of Biodiversity articles, including research from all fields plus associated magazine content, have now been published across the PLOS journals. With this healthy level of ongoing activity, the community has outgrown the original need for the Hub, which was created to give greater visibility to their previously widely dispersed content.

Rest assured that we are developing more powerful tools for our journals to help those working in this community rapidly find and filter Open Access content, and continue to seek novel ways to re-organize and present it for discussion.

If you have any specific questions please email our user services team.

Best wishes
The PLOS Publications and Products Team

Annual Notification: How to File Whistleblower Reports (#UCDavis)

Seemed worth wide distribution:

2013_Whistleblower_Poster_Revised_by_OP.pdf

At #UCDavis June 24: Mini-symposium on cancer genetics and admixture mapping-

MINI-SYMPOSIUM ON

CANCER GENETICS AND ADMIXTURE MAPPING

SPONSORED BY UC DAVIS HUMAN GENETICS AND GENOMICS

FOCUS GROUP AND THE CHIBCHA CONSORTIUM

Date: June 24, 2013

Location: GBSF 1005

CHIBCHA_flyer_061413_FINAL.pdf

ADVANCE Reading of the Day: Sylvia Earle, Women in Japan and the Gulf, Spaceflight

Quick post here … Some news stories and posts I am checking out today in relation to the UC Davis ADVANCE project in which I am involved.