Tag: Misc.

At #UCDavis 3/31 – Frontiers in Publishing: Experience w/ open access publishing

Thursday, March 31, 2016

PANEL: 3:00P.M. – 5:00P.M. RECEPTION: 5:00P.M. – 6:00P.M.

UC Davis, Activities & Recreation Center (ARC), Meeting Room 1

Frontiers is a leading Open Access scholarly journal publisher, with 55 journals in many disciplines and growing. In addition to rising journal impact factors, Frontiers is advancing article-level and author metrics as new ways of measuring the impact of research. A growing number of UC Davis faculty members edit Frontiers journals and have gained experience with this new publishing model and its benefits and challenges for publishing research. Join

us for a look at the benefits of Open Access publishing for improving research impact through increased citations, and a cross- disciplinary panel of five UC Davis editors, on how Frontiers has worked in practice.

Participants:

MacKenzie Smith, University Library (moderator)

Neelima Roy Sinha, Plant Biology

Cecilia Giulivi, Molecular Biosciences & Vet Med

Patrice Koehl, Computer Science & Genome Center

Mary M. Christopher, Vet Med Pathology, Microbiology & Immunology

Arne Ekstrom, Psychology

Sandra Hausmann, Frontiers

Frontiers event poster 03-31-2016.pdf

Letter from President Napolitano to UC community about new sexual assault measures

Of possible interest:

UNIVERSITY OF CALIFORNIA COMMUNITY

Dear Colleagues:

Recent developments have roused concerns and questions regarding how incidents of sexual harassment and sexual violence are addressed at UC. I want to take this opportunity to reinforce some important points and share with you additional measures I am instituting to address these issues.

Let me be clear: each and every one of you has the right to come to UC to learn and work in an environment free of sexual harassment and sexual violence, and to be part of an institution that deals with any substantiated reports of sexual harassment or violence firmly, fairly, and promptly.

Ensuring that UC is a safe environment is a top priority both for the University, and to me personally. In 2014, I formed the 29-member President’s Task Force on Preventing and Responding to Sexual Violence and Sexual Assault, which has spent the last two years instituting systemwide improvements to strengthen our processes and increase transparency and consistency across the system. These improvements have included mandatory education and training for students, administrators, faculty, and staff; confidential support for survivors; resources for people reporting sexual violence and those responding to allegations; and standardized procedures for investigating, adjudicating, and imposing sanctions in cases involving students.

In cases involving faculty, I appointed a joint committee of the UC administration and the Academic Senate, with student representation, to review our current procedures and provide recommendations to me by April 4. Once that work is complete, we will then focus on reviewing our process for handling cases involving staff beginning in April.

But recent developments have demonstrated that we must take immediate steps to further shore up our efforts.

Last week, I established a new Systemwide Peer Review Committee that will review and approve all proposed sanctions for any senior University leader found to have violated our UC Policy on Sexual Violence and Sexual Harassment. Senior leaders include, but are not limited to, Chancellors, Associate and Assistant Chancellors, Provosts and Vice Provosts, Deans, Coaches, and Athletic Directors.

After consulting with the Chancellors, I have appointed the following individuals to serve on the Systemwide Peer Review Committee:

• Co-Chair Sheryl Vacca, UC Chief Compliance and Audit Officer and Chair of the President’s Task Force on Preventing and Responding to Sexual Violence (UC Office of the President)

• Co-Chair Allison Woodall, Deputy General Counsel (UC Office of the President)

• Ramona Agrela, Associate Chancellor, Chief Human Resources (UC Irvine)

• Brian Alldredge, Vice Provost of Academic Affairs, Professor of Clinical Pharmacy (UCSF)

• Ken Baerenklau, Associate Provost, Associate Professor of Environmental Economics and Policy (UC Riverside)

• Gregg Camfield, Vice Provost for the Faculty, Professor of Literature and Culture (UC Merced)

• Fiona Doyle, Dean of Graduate Division, Professor of Mineral Engineering (UC Berkeley)

• Julie Freischlag, Vice Chancellor of Human Health Sciences, Dean of School of Medicine (UC Davis)

• Margaret Klawunn, Vice Chancellor of Student Affairs (UC Santa Barbara)

• Sarah Latham, Vice Chancellor of Business and Administrative Services (UC Santa Cruz)

• JoAnn Trejo, Associate Dean of Faculty Affairs in Health Sciences, Professor of Pharmacology (UC San Diego)

• Patricia Turner, Vice Provost of Undergraduate Education, Dean of the Division of Undergraduate Education (UCLA)

In addition, I have directed the Chancellors to ensure that all senior leaders take the University’s mandatory sexual harassment training by March 25 to guarantee full understanding of UC’s policy and procedures.

We must, and we will, do a better job of investigating all claims of sexual harassment or sexual violence thoroughly and fairly. And when claims are substantiated, we must hold people accountable and impose sanctions that appropriately reflect the seriousness of these cases.

Yours very truly,
Janet Napolitano
President

UC_Community_Systemwide_Peer_Review_Committee_3181_0.pdf

The #UCDavis Chancellor’s Board Positions and the Need for a More Public, Open and Early Disclosure System

So, I assume by now many people out there have heard about the controversy going on at UC Davis over the board positions taken by the UC Davis Chancellor Linda Katehi.  If you have not – here is a brief summary.

  • In late February, Chancellor Katehi accepted a board position at the for profit educational company Devry but then steeped down after complaints.  See for example this story by Diana Lambert in the SacBee for details.  Note – she has admitted that her accepting of this position prior to getting approval from the UC President was a violation of UC policy.
  • Chancellor Katehi received $420,000 in compensation for serving on the board of John Wiley and Son’s from 2012-2014.  See this SacBee story by Diana Lambert and Dale Kasler for more detail.  In relation to this report, Chancellor Katehi has apologized and has said she will donate “all the stock proceeds” she made from Wiley to a Scholarship fund for UC Davis students.
  • Chancellor Katehi served on the International Advisory Board of King Abdulaziz University in Saudi Arabia for a year.  This is the same University that has been strongly critiqued for its practice of paying highly cited scholars to become adjunct faculty in order to boost its ratings. It has been reported that she did not attend any of the board meetings in person and did not receive any compensation for this.  See this and this for more detail.  
There have been many responses to these revelations including:

The situation does not appear to be letting up.  I note – in the description above I have tried to be as objective as possible in describing the situation.  And I have been thinking a lot about what I think should happen now.  Do I think the Chancellor should resign?  Should she be fired?  Do we need more faculty to come out in support of her?  What is the best path forward for UC Davis?  I certainly have thoughts on these questions and related topics.  And I assume many people who know me know that I am not exactly shy about expressing my thoughts in public.

But … there is one major thing that gives me pause here.  And it relates to the comment above about trying “tried to be as objective as possible” here.  The reason this gives me pause here is because one of the key issues at play relates to “Conflicts of Interest” – both real and perceived – in the Chancellor’s board positions.  Many critics have argued that each of these board positions comes with major conflicts of interest in the Chancellor’s job as the head of a major public university.  The Chancellor’s supporters have argued that these board positions at worst involved the appearance of a possible conflict and not any real conflict.

Why I am digging into this conflict of interest topic?  Because I think one key way to help people assess whether there are any real or possible conflicts of interest in one’s activities is to fully disclose as much as possible about one’s activities.  And I think the UC in general and the Chancellor of UC Davis could do a much much much better job in terms of disclosures.  And I have a proposal for that.

But before we get into that I think it is necessary for me to make some disclosures.  Here are some:

  • I am a Professor at UC Davis
  • I have worked on a few projects with the UC Davis Chancellor Linda Katehi directly and indirectly and I have always had positive interactions with her).
  • I have worked on the UC Davis ADVANCE Project ( to increase the participation and advancement of women in academic science and engineering careers) for which Chancellor Katehi is the lead. 
  • I don’t always agree with actions taken by Chancellor Katehi but I do believe she is truly committed to improving UC Davis
  • I have worked for many years on “open access” to scholarly literature (and a little bit to textbooks) and have occasionally been at odds with the John Wiley and Son’s company.
  • I was involved in an exposé of what I believe to be unethical behavior of King Abdulaziz University a few years ago in their attempts to buy rankings by trying to have scholars change their institutional affiliations on publications and in citation databases.  See for example this and this and this.  I note – I was threatened by one of the people from KAU who I helped expose.  I am NOT A FAN of KAU.
  • I spent almost two months writing about the pepper spray incident and follow up in 2011 in an effort to help save the image of UC Davis, which I love.  See some of my posts about this here.  The whole incident and the aftermath was very traumatic for the University and many individuals associated with the University, including myself.  There were calls for Chancellor Katehi to resign then.  And there were statements of support by deans and faculty.  I refused to sign either.  I thought she and the UC Davis admins made many mistakes and did not by any means deserve endorsements.  But I also thought it was unclear if their mistakes were enough for them to be pushed out. 
  • Other disclosures of mine are here: https://phylogenomics.wordpress.com/about/disclosures
I have listed these disclosures because I am not sure I can be objective about this story.  And I want everyone reading this to have this information so that you can make your own decision as to whether you think my possible conflicts of interest might cloud my judgement in various ways.  I tried to be objective in outlining what I think the current state of the situation is above, but I understand that not everyone may agree.  And if people think my view of the situation is too biased, well, they probably will not care too much about what I think we should do now.  And I am OK with that.  What I want most is for people to know now just what my positions are, but what might have affected what my positions are.

OK – so that is a way longer introduction than I had imagined in getting to the question of “what should we do now?” 

A reader who thinks I am not completely compromised might ask – what do I think about the situation and what do I think should happen now?  Here are some comments:

  • I personally think that accepting each of these board positions was really not wise.  Yes, the Chancellor may have accepted them with the best of intentions.  And yes, she may not have done anything inappropriate in her time on the two on which she served (Wiley and KAU).  But I think it would not have been that hard to imagine how these board positions might be perceived – especially by UC Davis students.  And that alone I think should have led to turning down these board positions.  She has admitted Devry was a mistake. She has not admitted (as far as I know) that Wiley was a mistake but has hinted that she can see how some people may not like it.  She has not admitted at all that KAU was a mistake as far as I can tell (and has defended it as being in the interest of promoting diversity), but given that it was known in 2011 widely that they were buying ranking in a seemingly unethical manner, this should have raised some red flags.  I do wonder a bit whether my really unpleasant interaction with KAU has made me more judgmental about this board position than maybe I should be (hence why I thought it was important to disclose this above).
  • Despite the above comments, I do not think that the board positions taken by the Chancellor are enough of a problem to call for her firing or resignation.  There are two major reasons for this.  My min reason for this is that I think one has to weigh the board position issue against all she has done as Chancellor and overall I believe she has done many very good things as Chancellor and that she is truly and deeply committed to UC Davis.  I understand that other people do not agree with this.  So I think in a way how people respond to this board position issue may relate largely to how good a job they think she has been doing as Chancellor.
  • I think a key mistake in this whole situation involved a poor job of disclosure.  More on this below.
  • I think another key mistake has been the slow and minimal communication with UC Davis and the public in response to these issues.  I really wish Chancellor Katehi and UC Davis administrators would hold some town halls or the like to discuss these issues and to explain to us why these board positions were taken.
So in summary – I think the Board positions were mistakes but I do not think they rise to the level of calling for the Chancellor to be fired or to resign.  I do think we should use this situation to completely revisit the topic of conflicts of interest, disclosure, and outside activities of the UC Administrators.  There have been calls, for example, to greatly limit if not stop entirely outside activities, especially at for profit entities, by the UC Chancellors and other higher ups.  I am not sure what I think about these calls, but they are definitely worth considering.  However, I think as a first step the UC could tackle one key issue – Disclosure.  

In general I think disclosures of possible conflicts of interest are done really poorly in academia.  So poorly that before this whole issue cropped up at UC Davis I made a proposal that scholars add disclosures to a centralized universal scholarly ID system known as ORCID.  See Improving Ability to Identify Possible Conflicts of Interest of Scholars 1: Adding a Disclosure Field to ORCID.  This would certainly help when on sees a paper by someone (say, Eric Lander) and would allow one to get more information about their possible conflicts of interest (say, billions of dollars in possible royalties for the institute one runs).  I think such a system would be very useful.  But it is not really enough for the issue at hand here.

So in order to at least get the UC started down a better path in terms of conflicts of interest and activities by UC administrators I propose the following simple steps (and I note – this are just some ideas and thoughts, not a well formulated system at this point).

Proposed Public, Open, and Early Disclosure System for UC Administrators.

  • This system should be applied to all top UC Administrators (UC President, Chancellors, Provosts, Deans, and possibly others)
  • Disclosures of outside activities and potential conflicts of interest must be made publicly available in a centralized location. 
    • This would include Form 700s and other declarations.
    • I have been told such forms are available for all UC Admins.  They are certainly not readily available.
    • UC Administrators should be required to update such disclosures quarterly
  • The disclosures need to be referenced and linked readily and widely:
    • The disclosures should be provided at the administrator’s profile pages 
    • Disclosures or links to them should accompany all official communications of these administrators (much in the way disclosures should accompany scholarly publications).
  • Administrators should be required to submit proposed outside activities to the public PRIOR to commencing those activities. 
    • There should be a public commenting period regarding these proposals
    • The specific activities and compensations must be included in all proposals
    • The proposals should include a discussion of the putative benefits to the UC for such activities.
    • There should be a more public, more formal review process for determining if the proposed activities are in the best interest of the UC
  • These disclosures should happen whether or not any other regulations about outside activities happen.
I understand this will not solve all the issues associated with outside activities, conflicts of interest, and such.  But I think one big step would be for the UC to adopt a more open, public, early, easy to find, and widely share disclosure system for outside activities of UC Administrators.  And perhaps, just perhaps, requiring such open, public, and early disclosure system would lead some UC Administrators to think more carefully and clearly about what outside activities they choose to do – or propose to do.
Update 3/23: some other links of relevance

Been attempting to get for 700s for the Chancellor (as an exercise, not to dig into them in any detail). Writing about it in a seagate post.

——–
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.

——–

At #UCDavis: Center for Open Science’s Open Science Framework 5/4/16

Workshop announcement: Open Science Framework

Who: Center for Open Science

When: May 4th, 2016

Times: 9 am – 12 pm (morning session) or 1 pm – 4 pm (afternoon session)

Pizza lunch at noon for both sessions

Where: DSI Space, Shields Library, room 360, UC Davis Campus

There are many actions researchers can take to increase the openness and reproducibility of their work. Please join us for a workshop, hosted by the Center for Open Science, to learn easy, practical steps researchers can take to increase the reproducibility of their work. The workshop will be hands­ on. Using example studies, attendees will actively participate in creating a reproducible project from start to finish.

Topics covered:

* Project documentation

* Version control

* Pre-Analysis plans

* Open source tools, such as the Center for Open Science’s Open Science Framework, which can be thought of as an electronic notebook that easily integrates the aforementioned concepts in a workflow.

This workshop is aimed at faculty, staff, and students across disciplines, who are engaged in quantitative research. The workshop does not require any specialized knowledge of programming. Participants will gain a foundation for incorporating reproducible, transparent practices into their current workflows.

The three hour workshop is offered at two times to facilitate busy schedules. As space is limited, please register here by April 4th if you plan to attend:

https://docs.google.com/forms/d/16HcMmFq0_tl5gg-hhlilkLo_7fQ8Rb-J1DrFg6Te80Y/viewform

If you register and are no longer able to attend, please contact Jessica Mizzi (jessica.mizzi) and let her know.

UCDavisPromotionalFlier

#UCDavis CBS Dean Candidate #3: Public Talk at 2:15 Today

Posting this which I got by email. Please consider attending if you have any connection to the College of Biological Sciences.

Dear Colleagues in CBS,

This is a reminder that the last Dean candidate (candidate D) will visit campus tomorrow Wednesday, March 16 and Thursday,March 17. Please attend the public forum. Thank you for your participation and input.

The CV for candidate D is available from the provost’s website: http://provost.ucdavis.edu/initiatives-and-activities/activities/er/index.html

Please attend the Dean Candidate Public Forum!

Wednesday MARCH 16

2:15 p.m. – 3:45 p.m.

Presentation Topic: Role of Biological Sciences in Research and Higher Education in the 21st Century

PLACE: Room 1030 in Gladys Valley Hall- see attached map for location of building

And map of the first floor- NOTE, in different lecture hall from last time.

Valley Hall is just south of Med Sci 1B. Valley Hall is in the Veterinary College complex. Please see attached map. The lecture hall is on the first floor- see pdf of floor map.

It is only a short walk from the parking lot by the stadium/genome center. I suggest carpooling, biking or walking. Bring a colleague along with you!

We value your input regarding the candidates. You may submit them directly to Provost Hexter at deancbssearch. Or you may submit them to any member of the Recruitment Advisory Committee, or to me Judy Callis (jcallis) or to the chair of the committee Dean Lairmore (mdlairmore). Comments regarding all candidates are due 72 hours after this visit.

After the last candidate, the audio recordings for all candidates will be available from the provost’s website.

Go to http://provost.ucdavis.edu/ On the left is "Executive Recruitments" Click on "Dean-College of Biological Sciences". The cvs are and audio recordings will be accessible from the menu on the right.

Valley Hall, Print Floor 1.pdf

Gladys Valley Hall map.pdf

UC-HBCU Initiative Event – 4/4 – Helping Faculty Prepare Underrepresented Students of Color for Doctoral Success

Got this in email and thought it would be of interest:

Dear Friends,

Could you please share the announcement below with faculty in your graduate program? Associate Professor Mark Jerng is the organizer of the event. There is great potential for these panelists to shed light on mentoring historically underrepresented graduate students for doctoral program success. Given the predictions of considerable growth and changing US demographics, this is an opportunity for faculty to dialogue directly with faculty colleagues from Hampton University, a historically Black university.

Best,

Josephine Moreno

************************************************************

Josephine Moreno, Ph.D.

Graduate Diversity Officer

Office of Graduate Studies

Humanities, Arts & Cultural Studies,
Social Sciences (HASS) and Education

Helping Faculty Prepare Underrepresented Students of Color for Doctoral Success

A Discussion of Teaching Practices and Institutional Structures

Monday, April 4, 2016

2:00 – 3:00 pm

Voorhies 126

This roundtable discussion addresses institutional structures of higher education and practices around preparing underrepresented students of color for doctoral programs. It features faculty members from Hampton University, a historically black university founded in 1868, who will share their experiences and expertise in teaching students at Hampton University and in advising and mentoring undergraduate research.

Our discussion will engage

· the teaching and mentoring of underrepresented students of color

· teaching and advising across different kinds of institutional spaces

· institutional structures and its impact on underrepresented students of color

· race in higher education

Panelists:

Dr. Amee Carmines, Department of English, Hampton University

Dr. Joyce Jarrett, Department of English, Hampton University

Dr. Mark Jerng, Department of English, University of California, Davis

Dr. Amee Carmines is Professor of English at Hampton University. Her academic focus is western and world literature and critical theory. During her twenty-nine year tenure at the university, she has served as faculty mentor to student fellows associated with the Dana Scholars Program, UNCF Mellon/Mays Undergraduate Research Program, and with IRT Fellows. She also routinely teaches central courses, such as literary criticism and senior seminar.

Dr. Joyce Jarrett holds the endowed chair of Distinguished Professor of English at Hampton University. She has taught a range of courses to include African American literature, senior thesis, advanced writing, and introduction to literary studies (a required tools course for majors). Currently, she also serves as a UNCF Mellon/Mays faculty mentor. Dr. Jarrett has also served the university in numerous administrative posts: Chair of the Department of English, Executive Assistant to the President, and Provost.

Dr. Mark Jerng is Associate Professor of English and Graduate Adviser for the PhD Program in English at University of California, Davis. He is Lead PI for the UCD Summer Program for Literary Analysis and Success in the Humanities (SPLASH).

This event is sponsored through the UCD Summer Program for Literary Analysis and Success in the Humanities (SPLASH), a UC-HBCU initiative that funds collaborations across the UCs and historically black colleges and universities. UCD SPLASH brings Hampton University undergraduates to UC Davis for an 8-week summer program during which they work with faculty mentors and develop independent research projects. The goal is to provide an undergraduate research experience as well as professionalizing activities in helping prepare students for applying to PhD programs in English and literature programs.

—

April 4 UCD-Hampton U Roundtable Event.pdf

Janelle Ayres talk at #UCDavis on host-microbe-microbiome interactions

//storify.com/phylogenomics/janelle-ayres-talk-at-ucdavis-on-host-microbe-micr/embed?border=false//storify.com/phylogenomics/janelle-ayres-talk-at-ucdavis-on-host-microbe-micr.js?border=false[View the story “Janelle Ayres talk at #UCDavis on host-microbe-microbiome interactions ” on Storify]
——–
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.

——–

talk Friday at #UCDavis Richard Bonneau on microbiome-immune interactions

The Genome Center Systems and Synthetic Biology Seminar Series present:

Uncovering mechanistic connections between the microbiome and the Immune system: new experimental designs meet new computational methods.

Speaker: Richard Bonneau
Associate Professor
Department of Biology
New York University and the Simons Foundation

Date: Friday, March 18th, 2016, 10am – 11am
Location: 1005 GBSF

3/16 at #UCDavis Provost’s Forum: Chris Kelty on Open Access, Piracy, and the Scholarly Publishing Market

The Provost’s Forums on the Public University and the Social Good Wednesday, March 16, 2016

Open Access, Piracy, and the Scholarly Publishing Market

Christopher Kelty

Professor in the Departments of Information Studies and Anthropology, and the Institute for Society and Genetics, at the University of California, Los Angeles

Christopher Kelty pursues research in the cultural signi cance of information technology, especially in science and engineering. He is the author most recently of Two Bits: The Cultural Signifcance of Free Software (Duke University Press, 2008), as well as numerous articles on open source and free software, including their impact on education, nanotechnology, the life sciences, and issues pertaining to peer review and research in the sciences and the humanities. He is trained in science studies (history and anthropology) and has written about methodological issues facing anthropology today.

In his lecture, Professor Kelty will provide necessary context by reviewing the politics and history of the challenges of scholarly publication; how publishing ts into knowledge production; how publishers have come to be a key component in the scholarly ecology and the political economy that sustain both universities and individual academic work; and the emergence of open access research and its links to other similar movements and technologies. Building on this context, Professor Kelty will focus on the struggle of some academics to create a viable form of open access, and the under-theorized indifference of the majority of academics to the open access question. Using his own experience in shepherding an open access policy through the University of California’s academic governance system, he will identify some of the reasons open access is simultaneously desired and resisted, and reflect on the assumptions beneath this tension. He will conclude by reflecting on the idea that we may not want the open access we are going to get.

Lecture:

3 to 4:30 p.m.
Alpha Gamma Rho Hall Alumni Center

Reception:

4:30 to 5:30 p.m. Library
Alumni Center

Sponsors Include: The Of ce of the Provost and Executive Vice Chancellor, the Community and Regional Development Program, the Center for Science and Innovation Studies, and Science and Technology Studies

Kelty 3-16-16.pdf

Seminar at #UCDavis today: The concept of tolerance defenses in host-microbiota interactions

Resistance and tolerance are two ways an organism might interaction with a microbe. While this model has been been recognized for many decades by investigators interested in plant-microbe interaction, the emphasis for animal-microbe interactions has overwhelmingly centered on resistance, largely because of a focus on pathogens. Today’s seminar speaker has tried to enlighten a more broad perspective.

Janelle Ayers
Assistant Professor
Salk Institute
"The concept of tolerance defenses in host-microbiota interactions”
Friday March 11
12:00 Noon
GBSF 1005