Open letter from the Academic Council to the UC (U. California) community

Just got this in my email with a comment to feel free to disseminate it widely.  So here goes:

Open letter from the Academic Council to the University of California community

 

We are the Academic Council of the University: we are the chairs of the ten campus divisions, as well as the chairs of the systemwide committees. We write to address the protests on many of UC campuses over the Regents’ decision to increase student fees by $2,500 per year. This decision followed budget shortfalls that have entailed significant staff layoffs and cuts to a range of student services. Faculty and staff also are suffering from significant reductions in compensation due to the current year’s salary reductions and furloughs.

 

We share the anguish over the policies adopted in the face of the state’s abrupt 20% disinvestment in higher education. The budget shortfall wounds the institution and community we cherish. We believe these policies are a regrettable but necessary response to the state’s actions. While we are committed to doing everything we can to mitigate their effects on the most vulnerable populations of our students and staff, we recognize that many disagree deeply, and that vigorous and vocal protest is an understandable response. The passionate advocacy of students, staff, and faculty for the University and its public mission has been remarkable.

 

Many of the protest activities were appropriate forms of peaceful advocacy. We are concerned, however, about activities at several campuses that disrupted our educational mission and interfered with the freedom of fellow students, faculty, and staff, to teach, learn, research, and work. We are especially concerned about group protests in which a number of individuals attempted to move past police barricades, physically threaten and throw objects at police, and surround vehicles to trap those within. These activities are unlawful and disrespectful of the rights of others, and they create a serious risk of violence for everyone in the area: police, protestors, and bystanders. A number of injuries, some serious, were sustained last week by both protestors and police officers.

 

We will insist, through all avenues open to us, that uses of force by police will be subject to inquiry and review, as well as the policies that govern crowd control. While we expect campus police professionals to be committed to accommodating peaceful protest, we realize that there may be failures of policy or individual action. We are committed to ensuring that the University remains a place where it is safe to teach and learn – and engage in peaceful protest.

 

At the same time, we wish to remind everyone of the limits of protest, and of our obligation to be civil, to show respect for different points of view, and to take personal responsibility for our own and each other’s safety. Occupation of university buildings, for example, directly interferes with the rights of other members of the community.

 

The problems that confront our University are daunting, and finding solutions to them will require the collective best efforts of our students, faculty, staff, and members of the community. Tempers will worsen and patience will shorten as these policies take hold, but we must channel our energies outwards, towards advocating for restoring funding to the University of California so that it can fulfill its mission of providing democratic access to the great research universities of our state.

 

Sincerely,

 

 

Henry C. Powell, Chair

Academic Senate

 

Daniel L. Simmons, Vice Chair

Academic Senate

 

Christopher Kutz, Chair

UC Berkeley Divisional Senate

 

Robert Powell, Chair

UC Davis Divisional Senate

 

Judith Stepan-Norris, Chair

UC Irvine Divisional Senate

 

Robin L. Garrell, Chair

UCLA Divisional Senate

 

Martha Conklin, Chair

UC Merced Divisional Senate

 

Anthony W. Norman, Chair

UC Riverside Divisional Senate

 

William Hodgkiss, Chair

UC San Diego Divisional Senate

 

Elena Fuentes-Afflick, Chair

UC San Francisco Divisional Senate

 

Joel Michaelsen, Chair

UC Santa Barbara Divisional Senate

 

Lori Kletzer, Chair

UC Santa Cruz Divisional Senate

 

Sylvia Hurtado, Chair

Board of Admissions and Relations with Schools

 

Farid Chehab, Chair

Coordinating Committee on Graduate Affairs

 

M. Ines Boechat, Chair

University Committee on Affirmative Action and Diversity

 

Alison Butler, Chair

University Committee on Academic Personnel

 

Keith R. Williams, Chair

University Committee on Educational Policy

 

Shane White, Chair

University Committee on Faculty Welfare

 

Gregory Miller, Chair

University Committee on Research Policy

 

Peter Krapp, Chair

University Committee on Planning and Budget

Bay Area Biosystematists: 12/8, John Carlos Garza on Genetics & mgmt of California fishes

The Bay Area Biosystematists present:
 
“The use of genetic data to delineate management units for California fishes”

John Carlos Garza
Southwest Fisheries Science Center, NOAA
and
Dept. of Ocean Sciences, UC Santa Cruz

As lead of the Molecular Ecology and Genetic Analysis (MEGA) Team, Dr. Garza and his lab
use population genetic data and analytical techniques to address a broad array of questions in ecology,
evolution, behavior, conservation, and management of marine and anadromous organisms. This talk will focus on identifying management units for California fishes and their relationship to taxonomic units

For more about Dr. Garza’s work, visit his website:
http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=902

Tuesday, December 8th, 2009
At the California Academy of Sciences
Golden Gate Park

Dinner and social hour begin at 5:30 pm              Delicious food!!      Thirst quenching beers and healthy sodas!!

Evening presentation begins at 7:00 pm

RSVP REQUIRED FOR DINNER OR TALK
Please rsvp to Healy Hamilton hhamilton — at —- calacademy.org

NSF looking for grants on "Life in Transition" re:climate change

Just got this email from the National Science Foundation saying that NSF is looking for more grants relating to responses of organisms/ecosystems to climate change.

The Divisions of Integrative Organismal Systems (IOS) and Molecular and Cellular Biosciences (MCB) in the Directorate for Biological Sciences at NSF encourage submission of proposals that address the biochemical, molecular, cellular, genetic and/or organismal underpinnings of adaptation and biological feedbacks to climate change.  Interdisciplinary and systems level approaches to these problems are encouraged. A cross-divisional working group has been established to ensure that exciting proposals in this area receive adequate and appropriate attention. 

Life on earth contributes actively to the forces involved in troposphere climate and chemistry. Not only are organisms key participants in climate and chemistry forcing functions, they are also highly sensitive to changes in many climatic and chemical properties of the troposphere.  Research is needed to understand the limits of biological adjustments to such changes, and the feedbacks on climate and chemistry that will result. 

The Foundation has a rapidly growing commitment to research directed towards understanding the interplay between living organisms and the earth’s climate and surface chemistry.  In the Directorate for Biological Sciences, this was emphasized last year by the establishment of a special Life in Transition activity, as announced in an open letter to the research community, accessible at: http://www.nsf.gov/pubs/2008/nsf08078/nsf08078.jsp?org=NSF.

Please consider submitting proposals of this kind to IOS and MCB using the ‘LiT:’ title preface described in the Life in Transition ‘Dear Colleague’ letter referenced above.  A project summary and introduction that place the proposed  research in the context of global climate change will be most helpful in determining appropriate sources of funding within NSF. 

If you seek further information, queries sent to this return email address will be directed appropriately to insure a prompt reply.

Worst new omics word award: Negatome

Last week I asked for people to post suggestions for bad new omics words as candidates for my “Worst new omics word award”. And there were some great ones posted there by MAT kinase (physiomics, orfeomics), Mr. Gunn (degradomics, though he noticed it was already suggested), anonymous (incidentalome), Karl Broman (human connectome), Paul (splicome), blJOg (Systemomics), Farhat Habib (resourceome), Rosie Redfield (sewa-genomics), Marmaduke (Microbial paleomics), and many others.

But by far and away, the worst of the worst, the most negative of all new omics words I have seen in a while, is the negatome suggested by multiple people. Yes, indeed, a group ( Pawel Smialowski, Philipp Pagel, Philip Wong, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Thomas Rattei, Dmitrij Frishman and Andreas Ruepp ) has written about, and even created a database for the negatome (for an excellent description about what the negatome is about, see The ‘negatome’ – a database of negative information… « mental indigestion (from Dr. Jim).

The concept of the negatome is good – it- “is a collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions”. It is meant in many ways as a database for testing various interaction measuring methods. And it could end up being quite useful. See Dr. Jim for more on its uses at the link in the previous paragraph.

But the name. Oh the name. It hurts to see. It hurts to say.

And thus,
… as suggested by GenomeWeb “Just watch out for Jonathan Eisen’s Worst New Omics Award.”
…and Iddo Friedberg on Twitter (@phylogenomics is going to love this one. The Negatome. Actually, quite useful.)
…and PSI Wavefunction on my blog) …
…and contrary to the suggestion by Ed Winstead on twitter who misinterpreted my twitter post about Iddo’s post when he said “Liked “The ‘negatome’ – a database of negative information” http://bit.ly/5ht98d even got the nod from @phylogenomics

…  Negatome the word is a winner of my coveted “Worst New Omics Word Award“.

Previous winners were:

My favorite evolution stuff 2. Charles Darwin Tobacco Card




In honor of Charlie D. I am posting one of my favorite Darwin items.  I got this from Ebay years ago.  It is a Darwin card – about 3 x 5 cm.  From Ogden’s Cigarettes, much like baseball cards.


Also see my previous “Favorite Darwin thing” – a post card from 1900 or so. 

Going on pump is like going back to school

OK – been on the pump now for about 1.5 weeks. Been OK. A huge learning curve here after 25 years of taking insulin shots. It feels a bit like I am going back to school. So much to learn. So much to unlearn.

Anyway. I am getting to know a few people on pumps too and they are an invaluable resource. What I find most amazing so far is how my kids, 4.5 and 2.5 years old, take this completely in stride. My 4.5 year old daughter now asks which pocket I am carrying the pump in so she can sit on the other leg. And she has asked if it is nice to not be taking shots anymore. Completely casual. Completely normal.
So far – my biggest challenges have been figuring out how to carry the pump and inserting the infusion sets. Getting the hang of the infusion sets (I am using a Medtronic pump currently with the Silhouette infusion system). Still no clue about how to carry the pump in diverse situations, like riding my bike in the rain … but I guess I will learn.

And the winner of ‘most nimble new science journal web site’ is mBio

Kudos to mBio the recently announced new open access journal from ASM. I posted a little bit about it a few days ago. There was some back and forth in the comments w/ people involved in the journal and, impressively, they have already modified some sections of the web site to clarify some of the things I and others felt were unclear. A pretty rare thing in the world of journals as far as I know, to make changes quickly. Normally there would be some sort of deliberative, painfully slow, and annoyingly conservative process in response to comments/feedback. Good job Barbara Goldman and ASM. And happy to have ASM moving a bit more towards an Open Access future.

For $&%# sake, Bentham Open Journals, leave me alone

For crying out loud, I am still getting crappy spammy mail from various “Bentham Open” journals. The most annoying part to me of Bentham Open is that they try to make it seem that anything published in an Open Access journal is better than anything published in a non Open Access journal. While I personally believe publishing in an OA manner is great, lying about the benefits of OA is not a good thing.

For example they ask and answer the following question “WHY PUBLISH IN OPEN ACCESS JOURNALS? ” Their answers include:

  • Your article will obtain more citations.
  • Your article will be peer-reviewed and published very fast.
  • Your article can be read by potentially millions of readers, which is incomparable to publishing in a traditional subscription journal.
  • All published open access articles will receive massive international exposure and as is usually the case for open access publications, articles will also receive high citations.

Yes, that is right, the crappiest, most boring, most idiotic article in an OA journal will receive “massive international exposure” and “high citations.”

I know, criticism of Bentham Open may seem biased coming from me, a PLoS insider. So, just in case you were not aware that just about everyone else out there cannot stand them, here are some reading assignments:

And so on.

Wanted – Bad New Omics Words

Blogger in need of material while taking a little break for medical reasons needs help. Seeking bad new “omics” words to give “Worst New Omics Word Award” to. Junkome from PZ Myers already under consideration. Please post suggestions here.

Previous winners are

Biologists rally to sequence ‘neglected’ microbes : Nature News

UPDATE: Our paper on this topic is out and there has been a bit of news here and there about it (e.g., NyTimes).  For more see

—————————-
Nice little story in Nature News about the need to sequence “neglected” microbes.

Biologists rally to sequence ‘neglected’ microbes : Nature News

Quotes me and a few others. Love the fact that it quotes Steven Giovannoni in support of this notion:

“The broad brush strokes of microbial diversity are not adequately represented in that first thousand,” says Stephen Giovannoni, a microbiologist at Oregon State University in Corvallis. “It’s absolutely important that we sequence more.”

I like this because Steve gave me enormous grief about this project at a conference last year. Though I argued with him and disagreed with him, his critiques helped guide much of our work on this project that helped make our paper on the work (which is in press) much better. Glad he generally is now in support of this type of project, though not sure what he thinks about our work in this area …

Here are some of my quotes:

“There’s no doubt to us that filling in the branches of the tree is going to be useful to lots of scientific studies that use genomic data,” says Eisen. “There have been four billion years of evolution and we can really benefit from having some of that information in our databases.”

All these new genomes should improve researchers’ understanding of the evolution, physiology and metabolic capacity of microbes, says Eisen. They will also help match DNA sequences to their proper species from large-scale, high-throughput metagenomic studies from environmental samples, and ultimately contribute in the fields of synthetic biology and genetic engineering.