Category: Misc.

Science Magazine Special Issue on H5N1 #Links #Microbes

"As a service to the community, AAAS is also making these articles free to the public. "

Would be nice to make ALL of Science available to the public but AAAS is a dinosaur of sorts. Anyway — at least these are available. (Thanks to Eileen Choffnes for the links).

H5N1: Bruce Alberts

Science 22 June 2012: 1521

http://www.sciencemag.org/content/336/6088/1521.full.pdf

Benefits and Risks of Influenza Research: Lessons Learned: Anthony S. Fauci and Francis S. Collins

http://www.sciencemag.org/content/336/6088/1522.full.pdf

Implementing the New U.S. Dual-Use Policy:Carrie D. Wolinetz

http://www.sciencemag.org/content/336/6088/1525.full.pdf

Evolution, Safety, and Highly Pathogenic Influenza Viruses:Marc Lipsitch, Joshua B. Plotkin, Lone Simonsen, and Barry Bloom

http://www.sciencemag.org/content/336/6088/1529.full.pdf

Influenza: Options to Improve Pandemic Preparation : Rino Rappuoli and Philip R. Dormitzer

http://www.sciencemag.org/content/336/6088/1531.full.pdf

Perspectives

Regulating the Boundaries of Dual-Use Research – Mark Frankel http://www.sciencemag.org/content/336/6088/1523.full.pdf

Securing Medical Research: A Cybersecurity Point of View : Bruce Schneier http://www.sciencemag.org/content/336/6088/1527.full.pdf

Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets (2012). Sander Herfst et al. http://www.sciencemag.org/content/336/6088/1534.full.pdf

· Materials/Methods, Supporting Text, Tables, Figures, and/or References Download Supplement

The Potential for Respiratory Droplet–Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host. Colin A. Russell et al. (2012). http://www.sciencemag.org/content/336/6088/1541.full.pdf

· Materials/Methods, Supporting Text, Tables, Figures, and/or References Download Supplement

Quick summary of session at #ASM2012 on “The Great Indoors” #microBEnet

 The session at the ASM 2012 meeting on “The Great Indoors” seems to have gone well. I will be writing up a more detailed report but here is a quick summary done via “Storify”.

http://storify.com/phylogenomics/asm2012-microbenet.js[<a href=”http://storify.com/phylogenomics/asm2012-microbenet” target=”_blank”>View the story “Session at #ASM2012 on The Great Indoors: Recent Advances in the Ecology of Built Environments ” on Storify</a>]

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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.

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Some notes from GSC13 session on microbiology of the built environment #microBEnet

At the GSC13 meeting a few months ago there was a session on microbiology of the built environment which was sponsored by my microBEnet project.

Posting some details from the meeting here.

Meeting notes and reports

Talk videos:

Paula Olsiewski

  http://www.scivee.tv/flash/embedCast.swf

The Indoor Standards – What Parameters Do We Need to Record? Jeffrey Siegel (University of Texas at Austin, USA)

http://www.scivee.tv/flash/embedCast.swf

Minimal Metadata for the Built Environment: A MIxS Extension Lynn Schriml (University of Maryland, USA)

http://www.scivee.tv/flash/embedCast.swf

The Home Microbiome Project: Unraveling the Relationship Between Human-associated and Home-associated Microbial Signatures. Jack Gilbert (University of Chicago/Argonne National Laboratory, USA)

http://www.scivee.tv/flash/embedCast.swf

The Indoor Virome! Scott Kelley (San Diego State University, USA)

http://www.scivee.tv/flash/embedCast.swf

The Role of VAMPs in the MoBEDAC Initiative Mitchell Sogin (Marine Biological Laboratory, Woods Hole, USA)

http://www.scivee.tv/flash/embedCast.swf

MoBEDAC – Handling Fungal Data From MicroBE Jason Stajich (University of California, Riverside, USA)

http://www.scivee.tv/flash/embedCast.swf

MoBeDAC – Integrated data and analysis for the indoor and built environment Folker Meyer (Argonne National Laboratory, USA)

——–
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.

——–

Coming up at the #ASM2012 mtg. "The Great Indoors: Recent Advances in the Ecology of Built Environments"

The American Society for Microbiology meeting is starting tomorrow and there are multiple things related to microbiology of the built environment there.  These include a session that was organized by Brendan Bohannan which I am chairing.

The details of the session are below:

Session Title: The Great Indoors: Recent Advances in the Ecology of Built Environments

Session Date/Time: Sunday Jun 17, 2012 3:00 PM – 5:30 PM

Session Room: Esplanade Ballroom 300

Description: Although humans in industrialized countries spend nearly 90% of their time in enclosed buildings, we know very little about the biology of the indoor environment. However, this is starting to change. Over the past few years, the field of indoor ecology has grown dramatically. Ecologists are beginning to apply ecological theory and concepts to understanding buildings as ecosystems. A new understanding of the biodiversity of built environments is emerging, as well as a new appreciation of the importance of interactions between humans and non-human life indoors. The proposed symposium will showcase this emerging understanding. We will feature presentations that demonstrate the utility of ecological theory for understanding built environments, that describe the dynamics of biodiversity indoors and that illustrate the interactions of humans with indoor ecology. Our focus will be on the ecology of the dominant forms of non-human life indoors – microorganisms – and their interactions with humans.

 Talks

  • Jonathan Eisen microBEnet: the microbiology of the built environment network
  • Nicholas Be: Examination of the environmental air microbiome using deep sequencing
  • Katie Kirsch: A microbial analysis of environmental surfaces in hotel rooms
  • Mark Hernandez: Stability of airborne microbes to master environmental variables
  • John Senko: Microbial communities associated with flue gas desulfurization systems
  • Kimberly Ross: Drinking water delivery networks as microbial ecosystems
  • Jordan Peccia: The effect of environmental conditions on the allergenic potency of Aspergillus fumigatus spores
——–
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.

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Pics from the Redrum hotel in DC where we stayed for #SAMG12

Img_3376 Img_3369

Img_3357

See the full gallery on Posterous

IMG_3368.MOV Watch on Posterous

IMG_3362.MOV Watch on Posterous

IMG_3370.MOV Watch on Posterous

IMG_3377.MOV Watch on Posterous

IMG_3371.MOV Watch on Posterous
——–
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.

——–

Updates on the #UCDavis Academic Freedom situation

A few days ago I wrote a post: Report on “Egregious Academic Freedom Violation” at #UCDavis.  The post provides some detail on an investigation carried out by the UC Davis Academic Senate into a case of apparent retribution at the UC Davis medical school.  In the case the Dean of the Medical School (Claire Pomeroy), the Executive Associate Dean Fred Meyers and the Health System Counsel appear to have carried out a retribution of sorts against a member of the faculty at the medical school (NOTE – I have a half appointment at the medical school).  The faculty member – Michael Wilkes had the gall to write an editorial (with Jerome Hoffman) for the SF Chronicle expressing opinions about a medical issue and actions of some people at the UC Davis Medical School.  Apparently, some people at the medical school did not like being criticized.  The result?  A threat to take away his space, to remove him as instructor of a medical school course, and other incites including a threatening email/letter from the medical school counsel.  Lovely.

Fortunately, the UC Davis Academic Senate was brought into the case by Wilkes and a committee of the academic senate responded VERY strongly with a report (see my previous post with more detail).  Meanwhile – news of the report spread and was covered in Inside Higher Ed.  It was then that I heard about it and felt the need to blog about it.  And news has spread a bit more (thank you PZ Myers and others).  On Friday, the UC Davis Academic Senate met (and though I am not a member of the Senate, I went to the meeting).  And the Senate passed three resolutions coming out strongly in support of Prof. Wilkes and critiquing the behavior of the Dean, Asst. Dean and Counsel from the Med. School.  Just after the resolution was passed the faculty received an email from the Provost Ralph Hexter that was very strongly saying he supported academic freedom on campus.

So that is where we stand now.  I am very pleased with the Provost’s statement.  At the same time I am still dismayed at the reported behavior of the Medical School administration.  And I think this issue needs to still get some air until there are repercussions for the Medical School actions …

Here are some related links and updates that I collected as the story has unfolded.



UPDATE: Some links of relevance

UPDATE 2: Some new links (6/8)

  • UC removes “In the media” page which linked to the Inside Higher Ed. story.
  • UC Davis Academic Senate passes three resolutions in relation to this case.  See here for full text.

UPDATE 7: 6/14

UPDATE 7: 6/15

UPDATE 8: 6/20

UPDATE 9: 6/25

UPDATE 10: 1/12/13

Well – finally some news.  Not sure what I think about it but at least something is moving forward.  A report was issued yesterday from a panel investigating this case.  
I have received a detailed email from Prof. Gregory Pasternack of UC Davis about the new “findings” from the report.  Pasternack was on the committee that issues the original report about this case.  He has this response to the new report:

1) Compared to the thorough 14-page analysis from the faculty investigation, the 2-page administrative review presents virtually no new information, contradicts the testimony of the Executive Associate Dean who said he was in fact responding to complaints against Dr. Wilkes, and completely ignores the totality of the threats all occurring peculiarly at the same time, creating a strong sense of retaliating when viewed as a whole. The faculty saw through thin excuses, while this review merely parrots and accepts them with no scrutiny or common sense. 

2) The administrative review claims a factual mistake in the timeline suggesting that the Executive Associate Dean wrote a key email before he was aware of Dr. Wilkes’ activities.  This is factually incorrect.  There is uncertainty about the timing of various emails (UC Davis does not keep historical emails, so a request for those went unfilled), but our report is very clear that Dr. Wilkes first raised his allegations to the Dean on September 16, 2010, well before the dates discussed by the administrative review.  Dr. Wilkes, other faculty, and the Dean were already well into the dispute when the Dean began retaliatory measures. Those measures continued over a period of time. The administrative review committee ignored this information. 

3) The administrative review appears to inappropriately downplay the seriousness of lawyers threatening faculty and fails to account for the fact that the lawyer was ordered by the administrators to send the threat to Dr. Wilkes.  Why are those administrators not held accountable for those orders?  According to the logic in the administrative review, if a person writes that they are not trying to interfere with a person’s academic freedom, then that grants free license to say and do anything, especially to violate faculty academic freedom. 

4) The fact that almost all administrative and legal personnel involved in the case have had adjustments to their University status since the Senate acted speaks louder than this poorly conducted and written review about what is going on. 

5) It is very disappointing that the administration will not apologize and move forward in a positive direction.

UPDATE 11:

UPDATE 12: 2/25/13

Just got this in email.  

Dear Academic Senate Members,
This message is being sent on behalf of Academic Senate Secretary, Abigail Thompson.  Please see the following link (http://academicsenate.ucdavis.edu/ra/RA-Meeting-Call-2013-02-28.pdf) to access the Representative Assembly Meeting Call forThursday’s (2-28-13) meeting.  You can also access RA information, meeting calls, and meeting summaries on the RA website (http://academicsenate.ucdavis.edu/repassembly.cfm).

On p9 of the document this is written:
Report to the Representative Assembly by CAFR – January 19, 2013
Last spring the Representative Assembly passed a series of resolutions related to academic freedom and the Provost sent a letter to the Senate in response. This report summarizes our analysis.

  1. In June 2012 the Representative Assembly unanimously condemned the use of letters from legal counsel to intimidate faculty: The provost has indicated that steps have been taken to prevent this, but stated that the actions of the administration cannot legally be described.
  2. In response to a thorough analysis by last year’s CAFR that found that the Medical School administration had impinged on the academic freedom of Michael Wilkes, the Representative Assembly unanimously requested in June 2012 that none of the actions threatened to punish Wilkes be carried out. To date, none of the actions have been carried out although none have been explicitly ruled out.
  3. In addition, the Representative Assembly unanimously passed a resolution calling for additional actions: an apology to Wilkes, training for medical school personnel on academic freedom and a report to the Representative Assembly with six months on the training program. The administration has elected not to do any of these things. The Provost has proposed a “town hall meeting” on academic freedom.
  4. The administration appointed a three person committee to examine the Wilkes case on their behalf. The committee’s report was provided with the letter from the Provost. There was only one new contention in the report; it called into question one piece of data in the CAFR report: the timing of one email threatening actions to be taken against Wilkes. Although put forward as a key issue, this is a secondary issue. Even assuming a revised timing of this email, the preponderance of evidence still supports the conclusions of the study conducted by CAFR last year and provided to the Representative Assembly, namely that the Medical School administration had impinged on the academic freedom of Michael Wilkes. 
——–
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.

——–

#UCDavis Provost Ralph Hexter very strong statement in support of Academic Freedom #Awesome

Just got this email in regard to the recent Academic Freedom Issue at UC Davis.

The following statement was issued today by UC Davis Provost and Executive Vice Chancellor Ralph Hexter:

In March, 1953 the Association of American Universities (AAU) adopted a statement articulating “The Rights and Responsibilities of Universities and Their Faculties.” It includes these words:

“A university must…be hospitable to an infinite variety of skills and viewpoints, relying upon open competition among them as the surest safeguard of truth. Its whole spirit requires investigation, criticism, and presentation of ideas in an atmosphere of freedom and mutual confidence. This is the real meaning of ‘academic’ freedom.“

A committee of our campus’s Academic Senate has devoted considerable time and effort to examining an assertion by a faculty member of the UC Davis School of Medicine that his academic freedoms were compromised by school administrators. Our Senate’s Representative Assembly earlier today heard and ratified the committee’s findings.

Academic freedom is sacrosanct at UC Davis, and the underlying assertions in this matter are deeply troubling. My office will review this case and take appropriate actions.

Some related links:

——–
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.

——–

New lab publication from Holly Bik: Microbial euks after gulf oil spill

New lab publication from Holly Bik: PLoS ONE: Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill.  Plus see associated Deep Sea News blog post with more detail: Dramatic impacts on beach microbial communities following the Deepwater Horizon oil spill

——–
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.

——–

Clinical Epidemiology & Study Design course announcement

Just received this announcement

Clinical Epidemiology and Study Design

The UC Davis Department of Public Health Sciences and the UC Davis Health System Office of Continuing Medical Education, in conjunction with faculty colleagues from the Department of Internal Medicine, is presenting a course in Clinical Epidemiology and Study Design from Monday, July 23, 2012 through Friday, July 27, 2012 (five days).

The principal instructors are Dr. Stephen McCurdy and Dr. Patrick Romano. The course is designed for new faculty, fellows, nurses, and interested persons beginning a career in clinical research.

This intensive one-week course in clinical research methods will cover developing a research question, study design, questionnaire design, data collection, data management, analysis and funding.

See attachment for further information

crseannoucemnt2012.pdf